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P E D S Y S USER`S MANUAL

1. EPDRAW Identify Ego position File MASTER XMP Enter a number above corresponding to C to continue to next step gt 12 Here the Example Master File was selected as the location of the pedigree records and the PID has been selected to identify EGO on these records Alternatively EGO Sequential ID could have been chosen When this selection has been made the program begins execution An example of the pedigree diagram produced from the output based on selections made above is shown below 34 8 e PREPDRAW May 4 1999 ID061 A A1A2 b 19720309 d 19980420 1D065 AB AA ID042 AB A1A2 b 19750000 d 19961114 b 19810705 d 19980116 1D045 A2A2 b 19820000 Q 1D071 A A1A2 b 19930318 If an unlinked file has been used to define symbols and or text fields Step 5 is skipped and the ID034 AB A1A2 b 19870623 K ID038 A A2A2 b 19740505 d 19961223 CE 1D055 1D063 A A A2A2 A1A2 b 19790000 b 19801128 ID070 1D077 A AB AA A1A2 b 19891012 1D049 B A2A2 b 19960908 following display appears to VIEW and to CONTI to SAVE file prepdraw tab and to QUIT NUE program execution b 19940923 1D056 A2A2 b 19731223 ID062 B A2A2 b 19800310 ID054 1D068 AB AA b 198612
2. O O Okll ooo no o Enter PID S lt n gt 1 32 lt n gt 1 32 or lt n gt to select record L to lock items to switch files F to find W to write record N for new file H for help Q to quit gt Note here that the file contains no records for sire or dam Commands Records for another individual and his or her parents may be selected by entering PID S lt n gt Entry of a valid PID brings up information for EGO FA and MO in parallel columns on the screen This option can be used only when a Master File or linked Data File has been selected where lt n gt is a Sequential ID Number For Master Files and unlinked Data Files lt n gt must be in the range 1 through lt nrecs gt where lt nrecs gt is the number of records in the file For Linked Data Files lt nrecs gt is the number of records in the Master File and is identical to the last Sequential ID Number in the file In the example above it can be seen in the status line at the top of the display that lt nrecs gt 32 Linked Data Files need not contain records for all individuals in the Master File which means that the number of records will not be the same as the last Sequential ID Number This is because the Sequential ID Number refers to entries in the Master File while the record counter applies to the Data File Entry of
3. If the table entry is correct the following display appears Enter A to create table automatically from genotypes phenotypes in FILE M to enter genotypes phenotypes MANUALLY for this locus At this point locus mnemonics have been entered into a new table and the next step is to add pheno types and their corresponding genotypes Option A Automatic creation of map table locus data read from file If option A is chosen the following confirmation display appears showing correspondences between phenotypes found in the file and their genotypes deduced by program GENOMAP ADA PHENO TYPE Genotype Phenotype Map AUCD Phenotype Genotype A A AB A B AC A C PRB B B BC B C E CAC Enter C to continue if this is correct E to edit R to restart with new locus gt c lt lt Note that you can t quit if you select R and then change your mind gt gt Here entry of E switches to Edit Mode see below R aborts the current entry and starts the be ginning sequence for entry of a new locus C produces the following display Genotype Phenotype Map Table 1 ADA PHENO TYPE Enter V to view locus E to edit locus A to add locus D to delete locus C to continue generating and saving output file gt June 10 1999 GENOMAP e 21 3 Here entry of V returns to the confirmation view of correspondences betwee
4. Are these correct Y N y Enter symbols for ALLELES in any order Enter RETURN alone when done Enter symbols for PH ES in any order ETURN alone when done gt A 2B gt AB gt O gt Next correspondences between phenotypes and the possible genotypic combinations derived from the alleles entered above must be established in the same manner as was illustrated above for the case in which data were read from a locus file June 10 1999 GENOMAP e 21 5 Locus ABO PH E Mode of inheritance AUDR Phenotypes 1 A Genotypes 1 a a 3 a o 5 b o A 2 a b AB 4 b b 6 0 0 Enter number corresponding to GENOTYPE to be assigned to a phenotype Enter AP to add DP to delete a phenotype AA to add DA to delete or RA to replace allele symbol Enter M to change locus mnemonics I to change mode of inheritance C to continue gt 3 Enter number of PHENOTYPE for a o gt 1 In the display above correspondence between the first two genotypes listed a a and a b and their respective phenotypes A AB have been entered while matching of genotype 3 a o with phenotype 1 A has been specified When this process is finished the program reverts to the same sequence of operations as shown above for other map table entry options confirmation display etc T Editing a previously created Genotype Phenotype Map File Entr
5. Identify EGO and parents gt Enter numbers above corresponding to ID of EGO FATHI ER and MOTHE When these individuals have been identified or if standard mnemonics are found the following display appears from which items are selected for inclusion in the output file At least one item must be selected May 21 1999 COUNTPED 12 1 EGO SEQUENTIAL ID 8 ER OF OFFSPRING Dam s Permanent ID SIRE S SEQ 9 PATERNAL SIBSHIP SIZI Sex M F or U DAM S SEQ 10 MATERNAL SIBSHIP SIZ Exit Date YYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI Exit Code EXT PATERNAL SIB S 12 EGO Permanent ID Pedigree ID Number EXT MATERNAL SIB SI 13 Birth Date YYMMDD Generation Number EX L SIB SEQ 14 Sire s Permanent ID ate s Permanent ID Items to be included File MAST Enter numbers corresponding to the items to be included in the output file Pedigr Number Generation Number and Pedigree Size will be added to the end of each record Enter A to select all C to continue gt When this selection has been made the following display appears Assign individuals that have neither parents nor offspring 1 All to the same pedigr Pedigr 0 2 Each to a separate pedigr Enter number corresponding to choice gt If EGO s record
6. ID061 19720309 SUBDIVIDE Item D to DELETE M 19980420 1 ID042 change MNEMONIC T to change change WIDTH of Item R to display an alternate RECORD SAVE and EXIT numbered item Data TYPE When an x is entered under these conditions the following display appears EGO Permanent ID Birth Date YYYYM Sire s Permanent I Dam s Permanent ID 5 Sex M F or U 6 Exit Date YYYYMMDD 7 Exit Code 8 Mate s Permanent ID EDIGREE NUMBE ENERATION NU EMIZE Select Standard Mnemonics File examped A Standard Mnemonic required for Master File is missing corresponding to BIRTH RETURN alone to skip field gt 2 24 8 ITEMIZE Enter number April 20 1999 Item 2 has been selected here and the correct mnemonic will be substituted automatically The pro gram proceeds through any other missing Standard Mnemonics and when all corrections have been made writes output files itemize out and itemize cde ITEMIZE employs some simplifying conventions in generating its output Code File a Only one mnemonic word may be entered for each data item defined If an input Code File has been used any change in mnemonics results in the new single mnemonic completely replacing all the original mnemonics b When a new Code File is generated any mnemonic entered is used also as the item descriptor label Wh
7. AUCD 32 32 158 168 158 170 158 L7 158 18 164 17 166 17 168 17 168 17 168 18 170 17 170 17 170 18 170 18 176 18 180 18 o o ooo oo ooo oo o ED gt Oy Sa CDI IDE o o o o o 50 o ooo oo oo oo KS Inferred types excluded o OO OH Ur ba WF Note that nine alleles and 15 genotypes are shown Compare this table with the one below derived from the same locus after it has been processed by DOWNCODE with reduction to five alleles speci fied D1S 3721 DWNCDE Phenotype Count AUCD 158168 158170 158176 158180 168170 168180 170170 170176 170180 176180 180180 UNT BLANKS Inferred types excluded INFE UNI o o o ooo ooo oo o 1 1 3 1 4 2 3 6 5 5 1 0 0 0 0 Here it can be seen that the number of alleles has been reduced to five and genotypes to eleven Tabular reporting of DOWNCODE processing is also given in file downcode tab as shown below again for locus D153721 April 19 1999 DOWNCODE e 17 5 DOWNCODE results for D1S3721 Starting with 9 alleles and 14 informative tripl Allele 164 was changed to allele 166 Leaving 8 alleles and 14 informative tripl 178 was changed to allele 186 Leaving 7 alleles and informative tripl 166 was changed to allele 186 Leaving 6 alleles and informative tripl 186 was changed to allele 180 Leaving 5 alleles and informative tripl
8. is exactly equivalent to the following sequence IF gt 16 ne F AND gt 16 ne U OR gt THEN gt 16 1 ELSE gt NEWITEM recognizes the full sequence skips the remaining prompts marks the item to be changed and waits for the next entry when RETURN is entered at the end of the line The second shortcut reduces the number of separate command sequences required for testing a single item against multiple test values That is multiple test values enclosed in square brackets and separa ted by commas may follow a logical operator A single sequence may be written for this case IF 12 EQ ID071 ID049 ID045 ID034 When the initial operator is EQ commas separating test values are interpreted as OR operators so that the statement above is true when Item 12 EGO PID is the same as any one of the PIDs in the list For any other initial operator commas separating test values are interpreted as AND operators Thus the following statement IF 8 LT 9 10 11 is true when Item 8 NUMBER OF OFFSPRING is less than all the values of Items 9 10 and 11 PATERNAL MATERNAL and FULL SIBSHIP SIZE respectively This shortcut applies only to test values that is multiple item numbers may not be tested in this way Data types of test items are determined by the data types listed in the input Code File The constant designator can also be used with multiple test values For example IF 11 eq k 1 2 3 and IF 11 eq 9 K2
9. 2 digit number for earliest year to convert to 21st century date RETURN for 00 R to return to conversion choices Enter 2 digit number for latest year to convert to 21st century date Enter RETURN for 09 R to return to conversion choices gt In most cases all dates on a given record will be converted in the same way However different formats can be accommodated For example if Birth Date and then Exit Date have been selected for conversion the following display appears immediately after the format for Birth Date has been set Format of date representation for BIRTH Input YYYMMDD Output YYYYMMDD Same format for gt Entry of N returns the format selection display which need be used only if more than one date for mat is used in the input file New dates replace those selected for conversion except where constants are added to or subtracted from the original in which case new dates are appended as an item at the end of the record H Entry of H produces the following help display July 7 1999 DATES e 14 3 Here are some calendar date formats accompanied by examples of their respec tive representations of January 1 2000 PEDSYS Format Non PEDSYS formats recognized by program DAT YYYYMMDD YYYY month dd yyyy DDMONYYYY YYY F 20000101 2000 January 01 2000 01Jan2000 000 003 YYYMMDD yyy dd mon yyy yyy mm dd yyyyj 0000101 000 01 Jan 000
10. EGO SEQUENTIAL ID ER OF OFFSPRING 15 Dam s Permanent ID SIRE S S ERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB S EGO Permanent ID 19 Mate s Permanent ID EXT MATERNAL SIB SI Birth Date YYYYMMDD 20 PEDIGREE NUMBER 1 SIB SEQ Sire s Permanent ID 21 GENERATION NUMBER INDEX Items to be included File MASTER XMP WARNING Input is in Master File format EGO FA and MO will be re indexed but sibs and offspring will retain their original Sequential IDs Enter numbers corresponding to items shown above in the order they are to b included in indexed record Enter A to list all items shown above C to continue to next step gt This warning indicates the potential danger of a mismatch between Sequential IDs of EGO FA and MO which will be re indexed and those of sibs and offspring which will not Such a mismatch could occur if changes have been made to the input file after it was originally indexed Under these circumstances it is usually best a to eliminate the original Items 4 11 for inclusion in output records or b to produce a complete new Master File by restarting the program and selecting Choice 1 or 2 22 4 e INDEX April 19 1999 Indexing EGO FA and MO without produ
11. Enter number of the entry above or R to return to initial function menu gt 1 Deletion of a Master File results in removal of all its linked Data Files from DBFILES When this option is selected the following warning display appears ETE DBFILES entry ING Removing MASTER XMP will also cause the following linked Data Files to be removed from DBFILES QUANTGEN XMP SAMPLES XMP HEMOGLOB XMP Delete MASTER XMP from DBFILI gt May 27 1999 DBFILER 15 5 e Important warning DBFILER begins modification of DBFILES as soon as the last command in the EDIT ADD or REMOVE sequence has been entered Do not interrupt execution of the program before notification of successful completion of the changes is displayed on the screen This is particularly important when adding or removing a Linked Data File since these operations modify file DPOINT lt EXT gt as well as DBFILES Fa N Edit NOTE As mentioned in Note c Section 9 of Appendix A it is often useful to include a note on line 1 of DBFILES reminding the user of the name of the database its date of creation etc Text information of this sort can be added or edited with the N command EDIT Notes Master Master Files Linked Linked Data Files Unlinked Unlinked Data Files Sub directory Subdirectories Enter M to edit Master File Note to edit Linked File Note to edit Unlinked File
12. Method 1 Ascending and or descending genealogical trees of specified depth are assembled for each proband Optionally probands full sibs and or mates may be included Method 2 Initially a nuclear family unit parents full sibs mates and offspring is assembled for a single proband In subsequent steps family units are formed for each relative of the proband newly added in the previous step The Output File generated by both methods is ordered by Permanent ID and duplicates are eliminated so that individuals appear only once which may merge pedigrees when multiple probands are selected 1 METHOD 1 Ascending descending trees 1 500 probands 2 METHOD 2 Assembly of family units Single proband Q QUIT without executing program Enter number above corresponding to choice gt Method 1 If Method 1 has been selected the following display appears from which the source of proband IDs may be chosen Pedigrees may be constructed for 1 500 probands entered from 1 Keyboard 2 Unlinked File 3 EXAMPLE 4 LOCUS Sub directory Enter number above corresponding to the appropriate source of probands gt 1 Choice 1 Proband IDs entered from the keyboard Choice 1 shown above specifies that proband IDs are to be entered from the keyboard Before keyboard entry begins the form of the IDs Permanent or Sequential must be specified Enter P if
13. Notes e DOWNCODE evaluates each nuclear family for informative EGO FA MO triplets that is those in which the parental origin of EGO s alleles can be determined e A nuclear family contains as many triplets as there are members of the offspring sibship e The list of potential downcoding changes seen in the display above is sorted in order of increasing loss of information e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example downcode subset out Error Checking If DOWNCODE detects one or more discrepant triplets it creates error file downcode err Contents of this file are records showing PIDs and genotypes of EGO and each of EGO s parents An example of this file is given below DOWNCODE Error report for Error Demo Pheno Ego ID063 B2 E Sire ID038 D E ID042 C Ego ID068 B2 Sire ID062 ID047 E Ego ID069 B2 Sire ID054 E F ID068 B2 ID071 D Sire ID045 C E ID034 E Ego Files Input A Master File and a Data File having records containing genotypic or phenotypic data with associated Code Files The Data File need not be linked if it contains pedigree data or if the pedigree can be supplied by another file Recursive use of output files is permitted that is file downcode out may be used as input to program DOWNCODE 17 6 DOWNCODE April 19 1999 Output downcod
14. If files from Enter to switch cyclically from one LINKED file to the next have not been preselected initial entry of presents a File List which they may be chosen Enter N to select new files for display E to find a specific entry for an item Enter Enter Q to exit program Press RETURN to continue gt F Initiates the find function see below April 19 1999 BROWSE 8 3 Q Exits the program a Column locking By default all items in the record may appear in the display window in their original order de pending on the horizontal position of the window with respect to the record This default may be over ridden so that some items may retain a fixed position in the window Entry of L produces the following Item List Display EGO SEQUENTIAL ID ER OF OFFSPRING 15 Dam s Permanent ID SIRE S SE ERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SEQ ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ FULL SIBSHIP SIZE 18 Exit Code EXT PATERNAL SIB SE EGO Permanent ID 19 s Permanent ID EXT MATERNAL SIB SE Birth Date YYYYMMDD 20 PEDIGREE NUMBE EXT FULL SIB SEQ Sire s Permanent ID 21 GENERATION NU BROWSE File MASTER XMP Enter numbers corresponding to items shown above in the order they are to b assigned to loc
15. The newly generated index item for the individual selected will immediately follow that individual s Permanent ID in the output record All other items will be placed in the same order as they appeared in the input record Files Input 1 For Choice 1 3 any pedigree file having records containing a unique identifier for an individual and his or her parents sex and birth date For Choice 4 any file containing a unique identifier for each record 2 An associated Code File 3 The Standard Mnemonics File CODE STD April 19 1999 INDEX e 22 9 Output index out contains all records of the input file plus additional records created to represent missing or unknown parents and hypothetical offspring of mated pairs without progeny with items indices etc added as described above index cde defines the record structure of index out index err contains information on individuals that fail to pass checks of internal consistency at the individual and family level duplicate Ego PIDs wrong sex of parent offspring birth date listed as earlier than that of parent etc index mpt contains records in Master Pointer File format Program limits A maximum of four individuals ID EGO SIRE FA DAM MO plus one additional individual may be indexed at one time Input files must be formatted as described above INDEX will not run with a pedigree file of more than 8 000 individuals on the IBM PC or 60 000 individuals on the Macintos
16. are legitimate expressions April 19 1999 NEWITEM e 29 5 Substring values of character data input Data Type C may be tested in multiples as well IF 12 EQ 071 049 045 034 Here the numerical portion of EGO PID is tested with the result in this example data set being the same as the sequence testing PIDs shown above Substring searches are slow and should be avoided when rapid output is needed on e Equivalences As a convenience several command elements have been given equivalent alternate forms These are EQ equal sign GT gt GE gt Or gt NE lt gt or gt lt LT lt LE lt or lt must be matched pairs D e Data Types PEDSYS programs require information about data types of items in input files defined by the data type codes listed in the input Code File These definitions are used by many programs to determine how data are to be interpreted However since PEDSYS Data Files contain nothing but ASCII text substring test values may be used whatever the Data Type specified in the input Code File For example if 13 eq k19661223 1973 then 17 k19880116 Here if Item 13 Birth Date is equal to the date 19661223 December 12 1966 or to any date beginning with substring 1973 any day during the year 1973 Item 17 Death Date will be set to 19880116 January 16 1988 Data types of output items in newitem out are determined by data types of the input
17. gt same pedigr using current The advantage of this restriction is illustrated by computation of kinship coefficients between opposite sexed pairs in the Humans 2 population listed in the table above Calculations for 13806 of these pairs using the Stevens Boyce method took 7 00 minutes Using PEDNO to identify pairs in which both individuals were members of the same pedigree limited calculations to only 478 pairs which took 2 56 minutes 25 8 KINSHIP April 20 1999 Algorithms A J Boyce Reference Boyce AJ 1983 Computation of inbreeding and kinship coefficients on extended pedigrees Journal of Heredity 74 400 404 Files Input Any Master File or indexed pedigree file and Master Pointer File Input Data File or console keyboard Output kinship out inbreeding contains Sequential and Permanent IDs of Ego Ego s parents and Ego s inbreeding coefficient kinship out kinship contains Sequential and Permanent IDs of the two individuals for which kinship was calculated and the kinship coefficient measured between them kinship cde defines the record structure of kinship out nokinshp out is an optional output file with the same format as kinship out but containing records for individuals or pairs with zero coefficients nokinshp cde defines the record structure of nokinshp out kinship err contains IDs of individuals for which calculations are requested but which were not found in the pedigree file
18. 31 32 EGO SUM COUNT MEAN STDDEV STDERR 00000 14573 59666 83582 39079 18678 76217 45477 74767 00000 31777 18868 23181 49172 37529 21139 15000 65000 D077 12 900 D080 187 900 D083 131 400 D097 175 800 D103 112 400 D109 133 800 D111 195 500 D113 26 500 D124 28 700 1 12 90000 13 14 45385 10 13 14000 13 13 52308 8 14 05000 10 13 38000 13 15 03846 2 13 25000 2 14 35000 H BRAH BE ALBA H H H N o o ooo oo o oo o o Wn O E H OO H O Enter lt n gt or lt n gt for new page lt n gt 1 27 to set top row gt or lt lt n gt to shift window I lt n gt 1 32 to set window L to lock columns N for new file F to find H for help Q to quit gt Note standard deviations and standard errors for individuals ID077 N 1 SD 0 ID113 N 2 SD 4 45477 and ID124 N 2 SD 3 74767 The next display shows results based on the adjusted standard deviation 9 4 e CALC April 19 1999 Items 32 Top record 18 27 31 32 STDDEV STDERR ADJ ADJ D077 12 900 D080 187 900 D083 131 400 D095 167 100 D103 112 400 D109 133 800 D111 195 500 D113 26 500 D124 28 700 1 12 90000 1 26833 13 14 45385 1 14573 10 13 14000 59666 13 12 85385 55017 8 14 05000 1 39079 10 13 38000 1 18678 13 15 03846 76217 2 13 25000 1 26833 2 14 35000 1 26833 26833 SLI 18868 15259 49172 37529 21139 8968
19. April 20 1999 ALTMASTR 5 1 1 Birth Date YYYYMMDD 4 Sex M F or U 7 Mate s Permanent ID 2 Sire s Permanent ID 5 Exit Date YYYYMMDD 8 PEDIGREE NUMBE 6 Exit Code 9 GENERATION NU 3 Dam s Permanent ID tai File MASTER XMP ALTMASTR Items to be changed Enter numbers corresponding to items shown above that are to be changed Precede item number with an H to carry over change of item from one record to the next Enter A or HA to change all items Enter C to continue to next step gt Note that a number of items normally found in a Master File are not presented in the display and cannot be modified These are EGO Permanent ID which is a fixed identifier of each record in the file as well as Sequential IDs and other items derived when programs INDEX or SETMASTR are run Items may be selected in the usual way so that only those that must be changed will appear on the Edit screen Additionally preceding numbers with an H for hold carries over the previously entered value to the next record to be changed or added This feature makes it unnecessary to re enter duplicate values on records of more than one individual The value displayed in the space provided for the item on the data entry screen will be added to the record unless it is changed or erased The new change or erasure will then be passed to subsequent records selected
20. April 20 1999 ALTMASTR e 5 5 Files Input In CHANGE Mode Any Master File having an associated Code File and Master Pointer File and CODE STD In START Mode An appropriately named Code File and CODE STD Output UPDATE lt EXT gt and or DELETE lt EXT gt Program Limits A maximum of 500 individuals may be ADDED to the Master File during any one session n 5 6 e ALTMASTR April 20 1999 ANCESTOR Program ANCESTOR identifies the closest common ancestors of all or a subset of probands and constructs the minimal pedigree linking ancestors and their proband descendants Two sources of input are required One is a file from which pedigrees are generated which may be either a Master File or an indexed pedigree file consisting of records containing IDs for Ego and Ego s parents Sex etc along with an associated Master Pointer File The other is a list of 2 to 200 probands entered from either the keyboard or from a Proband Input File a file consisting of a list of either Sequential or Permanent IDs Output consists of files containing a a list of ancestors common to a spec ified number of probands b a single pedigree linking all common ancestors with their proband descendants and c a pedigree for each ancestor and his or her proband descendants Introductory Display EDSYS program ANCESTOR Copyright 1992 1999 SFBR ANCESTOR identifies the closest common ancestors of all or a subset of probands and constr
21. Enter RETURN for Equivalence 1 or enter number of alternate selection precede number of selection with R to reverse Enter X to stop downcoding at this stage gt 1 The status line now reports that three alleles remain now that C is gone and that no informative triplets have been lost The list of potential changes shows that a change of allele D to allele A would result in the least loss of information When the change has been selected DOWNCODE reprocesses the data for this locus Since a second iteration is sufficient to achieve the desired number of alleles in the example no further displays are shown and the program then proceeds to the next locus if selected or writes its output files and terminates In some pedigrees rare alleles are informative and their loss by downcoding can be avoided by a Overriding the default order by choosing a higher numbered change or b Reversing the order of the change by preceding the number with an r For example entering r1 would result in changing allele F to allele C instead of changing C to F F To see the effects of DOWNCODE we choose as an example locus D153721 which is a more realis tic candidate for downcoding than that shown above Note first the table below which gives the 17 4 e DOWNCODE April 19 1999 distribution of alleles and genotypes and their respective frequencies for locus D153721 output of program GENEFREO D1S 3721 N Typed Genotype Count
22. Fe The pedigree diagram below shows these individuals and their relationships April 20 1999 KINSHIP 25 9 ID034 ID077 ID015 ID071 ID049 oO Proband Pedigree DrAw The following table gives all of the combinations specified by choices 1 3 in the pair composition menu and identifies the respective pairs in the pedigree for which calculations are done Pair combination Pairs for which kinship coefficients computed All opposite sexed pairs ID071 ID049 ID071 ID069 ID049 ID067 ID069 ID067 All same sexed pairs ID071 ID067 ID049 ID069 All pairs ID071 ID049 ID071 ID069 ID071 ID067 ID049 ID069 1D049 ID067 ID069 ID067 25 10 e KINSHIP April 20 1999 LIST Program LIST produces listings in a standardized format of any file for which an appropriate Code File has been constructed Designation and setup of printers for PEDSYS listings are controlled by the Device Control File DEVICES see Appendix A Introductory Display PEDSYS program LIST Copyright 1992 1999 SFBR LIST produces listings in a standardized format of any file for which an appropriate Code File has been constructed 1 Unlinked File 2 EXAI PLE da LOCUS Sub directory Enter number file name or Q to quit gt Because LIST does much of its formatting to conform to a particular output device the first action required is to select one of a series of output devices specified in file DEVICES Aftera file has b
23. Mother Father A A A B A C B B B C C E UNKNWN TOTAL Mother ID065 Offspring genotypes Father A A A B A C UNKNWN TOTAL A A May 21 1999 SEGCHECK e 37 5 Example 2 continued Mother Offspring genotypes Mother Father A A A B A C C C UNKNWN TOTAL Mother Offspring genotypes Mother Father A A A B A C B B C C UNKNWN TOTAL Example 3 Table configuration choice 3 separate tables for parental pairs grandparental phenotypes displayed tabulation without regard to offspring sex minimum 2 offspring of both sexes informative matings only inferred types included Segregation in FULL SIBSHIPS of at least 2 individuals MATINGS THAT SHOW SEGREGATION INFERRED PHENOTYPES INCLUDE LOCUS ADA PHENO TYPE ALLELES A B C Mother ID034 Phenotype Father Phenotype Fa s FA Mo s FA ID055 Phenotype A Mo s MO ID065 Phenotype AB Fa s MO Offspring genotypes A A A B A C B B C C UNKNWN TOTAL 37 6 SEGCHECK May 21 1999 Example 3 continued Mother ID065 Phenotype AB Father Phenotype A IDO61 1D042 Mo s FA Mo s MO Fa s FA Fa s MO Phenotype A Phenotype AB Phenotype A Phenotype AB Offspring genotypes A A A B Example 4 Table configuration choice 4 combined table of fathers with the same genot
24. Once an identifier has been selected and the file is sorted ALTERDAT Edit Add and Delete func tions are virtually identical to those described above for Linked files Commands O F L T and B Edit controls for an unlinked Multiple entry Data File Setting order of access confirmation status edit log template and audible warning for unlinked files is the same as that for Linked files Command N Create a new unlinked Multiple entry Data File Creation of a Multiple entry Data File that will not be linked to a Master File proceeds identi cally to the procedure described above for Linked Multiple entry files except that no Internal Pointer is appended to records as they are created Fi Notes e The number of multiple records for each individual is limited to 500 for the Unix and Macintosh implementations of PEDSYS 100 for the MS DOS version e Reserved mnemonics for two items control special features Random Order only An item with the first and second mnemonics DATE and UPDATE respectively will automatically be assigned today s date from the system calendar eliminating the need for keyboard entry of this information If these mnemonics are assigned automatic update occurs even if the item has not been selected for modification The item may have any label although common ones used are simply Date of Update Edit Date etc Editing an item with the single mnemonic COMMNT invokes a special instruction ID ID069 R
25. PEDSYS programs quite independently of a Master File or in fact without the existence of a Master File When a Data File is linked to a Master File the first item in each record must be the Ego Permanent ID mnemonic EGO or ID formatted exactly as it is in the Master File Subsequent items may be defined arbitrarily Single entry Data Files are normally created and updated with the PEDSYS program ALTERDAT but may be produced with any text editor or may be imported from other database systems b Multiple entry Data Files sometimes called Historical Files contain items for which more than one value is recorded during the lifetime of the individual body weight cage location etc A separate record is added to the end of this file each time an entry is made for the individual The first item in each record must be the Ego Permanent ID mnemonic EGO or ID formatted exactly as it is in the Master File subsequent Data items may be defined arbitrarily The last item is an internal pointer a number designating the location in the file of the previous entry for the individual This pointer takes the value 0 for the individual s first or only entry The internal pointer is an exception to the principle of including only data in PEDSYS Data Files However these fields may easily be ignored when using PEDSYS programs and may be skipped when information is exported to other programs because they are the last items in the record and are expl
26. 1992 09 27 1991 09 08 1997 11 30 ID049 1996 09 08 ID068 1988 08 31 ID070 1989 10 12 ID077 1994 09 23 I I I I I I T I I TL I I Ag I H BAH HAH HAH BHH HA EL AE HB HH Enter lt n gt or lt n gt for new page lt n gt 1 14 to set top row gt lt lt n gt to shift window I lt n gt 1 8 to set window L to lock columns file F to find H for help Q to quit gt or N for new Notes 11 6 COMBINE A blank field will be included in the output record if a blank is found in the input record Output records will be padded with trailing blanks as needed Order of access depends on the position of records in the input file The order in which records were entered in linked Multiple entry Files which may or may not be chronological can be recovered by sorting on the INTERNAL POINTER field The compound sort in program COMBINE provides control over which record will be first in the list for comparison The major sort is for the item or items selected for grouping records together but other items such as dates may be added as minor sorts so as to order records within groupings WARNING Care should be taken not to combine so many values that the output record becomes excessively long and unwieldy PEDSYS limits records to 1024 characters in length Combined records that would exceed this limit are truncated and a message is sent to the error log combine err The command line
27. DAM S SEQ EGO SEQUENTIAL ID FIRST OFFSPRING SEQ EXT PATERNAL SIB SE ATI EGO Bir EXT MATERNAL SIB SE EXT FULL SIB SI EQ O 0 JU SWNNF UMBER OF OFFSPRING ERNAL SIBSHIP SIZ Sex I oO O1 amp N OH FULI ERNAL L SIBSHIP SIZE Permanent ID th Date YYYYMMDD Sire s Permanent ID Dam s Permanent ID SIBSHIP SIZ M F or U Exit Date YYYYMMDD Exit Code ate s Permanen PEDIGREE NUMBER GENERATION NU Ego ID ADA Phenotype APOB Pvu2a Genotype Tot Ser Cholestero APOAI Level EPDRAW Palette 3 Alpha codes After IF gt enter lt Item o gt lt Operator gt lt Test gt TH IF gt 14 EQ UNT C Consultand Asterisk Negative Positive 26 b then b E G H THEN S B Enter H for explana IF gt 9 tion and shortcuts Double neg N g Pos F Pos Neg Double pos I J K L EQ K800101 TH Unassigned 1 Unassigned 2 Unassigned 3 Unassigned 4 EN SYMBOL lt symbol gt EN SYMBOL C C to continue M Unassigned 5 N Unassigned 6 O Unassigned 7 P Unassigned 8 In this example an asterisk Code B will placed in the center of symbols representing all individuals with an unlisted blank APOAI Level Item 26 Entries in Palette 3 differ from those of other palettes in that
28. If the length specified in the Code File is greater than the maximum record length found in the input Data File all items listed in the Code File are displayed on the screen with their numbers mnemonics and ruler As many characters as there are in the Data File are assigned to these items and are shown in the row beneath them Code File items for which there are no corresponding data are displayed with blank characters in the row beneath them Unless explicitly skipped these blanks are included in the output file itemize out and are defined in itemize cde The length of the longest record found in the file is greater than that specified by the Code File In this case characters from the input Data Record are assigned to as many Code File items as there are and the remainder are displayed as a single unformatted text string Checking for Standard Mnemonics If the option to prepare the foreign file for use as a PEDSYS Master File has been selected ITEMIZE checks to see that Standard Mnemonics EGO or ID BIRTH FA or SIRE MO or DAM and SEX have been designated If all are present ITEMIZE proceeds to write its output files However if one or more are missing an opportunity to assign Standard Mnemonics is provided As an example of the latter operation note that Item 2 in the display below DOB does not conform to the standard BIRTH examped Record 1 of 32 Length 48 1 2 ID DOB 6 7 EX EXIT EXCODE
29. PEDSYS programs Opt tech Sort is the copyrighted property of Opt Tech Data Processing P O Box 678 Zephyr Cove NV 89448 Terms of the license permit use of the routine in any authorized version of PEDSYS a Major support for the development of PEDSYS has been provided by NIH Grants RR02229 Genetics and Inbreeding in Nonhuman Primates and RR Support for programming personnel also has been provided by NIH grants HL28972 Diet and Genotype in Primate Atherosclerosis and GM31575 June 12 1999 v Genetic Analysis of Common Diseases An Evaluation si Copyright and Limits on Use The development of PEDSYS represents a substantial and costly effort that has been supported by research grants from the U S National Institutes of Health We feel strongly that it is unethical to sell the efforts of work funded from these sources to individuals or institutions also supported by public money Although we will provide PEDSYS to NIH grantees and non profit institutions or their equi valents in other nations at a fee covering only the costs of media shipping etc the package is not in the public domain The programs and manual bear copyright notices dated 1988 or later and are subject to the following conditions of use The programs may not be sold or incorporated into other software packages that are sold for profit nor may fees other than standard costs associated with data entry and computer services be charged for their use without th
30. RH RoR UH jb PO on N H H H H N H H H H H H H N OO amp on LL H HN 3 2 1 6 7 7 m A for next page number 1 32 to set top record Q to quit The starting record of the page sequence may be reset by entering the appropriate record number prior to the RETURN as indicated by the instructions at the bottom of the screen shown above 26 4 e LIST April 20 1999 The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example list subset out a Format options Program LIST permits records with a common attribute to be printed in distinct groups For example all animals having the same dam may be printed contiguously separated from other maternal half sibships by a blank line a dashed line or a page boundary This requires that the file be sorted by DAM Permanent ID or DAM Sequential ID prior to running LIST The Forms option produces boxes for handwritten entry of data or comments by enclosing records and item entries with dashed lines This format may be combined with the sorted group option des cribed above The number of items that will fit across a page is limited by paper width printer type size and item field widths The approximate number of columns available is the product of nominal paper width typically 8 or 14 inches and width of printed characters 1 10 1 12 1 15 1 16 6 inch etc LI
31. Setting the number of digits to the right of the decimal place to zero results in integer output The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example calc subset out 9 6 CALC April 19 1999 Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file calc out may be used as input to program CALC Output calc out contains all records in the input file in their original order each record contains all items from the input record in their original order followed by items containing calcula tions and numerical sequences in the order they were chosen When precision is changed items remain in their original position with their field width and Code File entry adjusted as necessary calc cde defines the record structure of calc out Program limits 50 new items results of calculations or numerical sequences may be added to records z April 19 1999 CALC e 9 7 9 8 e CALC April 19 1999 CODE Program CODE is used to create and or edit a Code File Introductory Display PEDSYS program E Copyright 1992 1999 SFBR Enter C to CREATE a new Code File E to EDIT an existing Code File O TO l program Create and Edit Modes in CODE are separate functions each having their own style of console entry Either mode may be se
32. Sex M F or U Tot Ser Cholestero Exit Date YYYYMMDD APOAI Level Exit Code EGO SEQUENTIAL ID SIRE S SEQ DAM S SEQ FIRST OFFSPRING SEQ PATERNAL SIB SE MATERNAL SIB SE FULL SIB SEQ ER OF OFFSPRING ERNAL SIBSHIP SIZ LU 0 JU amp N H JO O1 amp NN LO PREPDRAW Palette 2 Quadrants After IF gt enter lt ItemNo gt lt Operator gt lt Test gt THEN SYM IF gt 11 EQ A THEN SYMBOL A IF gt 12 EQ THE Enter H for explanation and shortcuts C to continue Trait 1 E Trait 1 Trait 1 3 Trait 1 2 4 Trait 2 Trait 24 Trait 2 4 Trait 1 2 3 Trait 3 Trait 3 Trait 2 34 Trait 1 2 3 4 Trait 4 Trait 1 Trait 1 34 unknown Last entry IF 25 LE K99 THEN SYMBOL IF gt 25 gt k99 then h 34 4 PREPDRAW May 4 1999 Here the line displaying the last entry specifies that the two right hand quadrants of symbols representing individuals with a total serum cholesterol greater than 99 will be filled Other quadrants and combinations of quadrants may be used to represent other phenotypes as well e Note Only one pattern from Palette 2 may be assigned to a single individual Selection of Palette 3 results in the following display page 2 shown here also SIRE S SEQ
33. That is it is given the mnemonic UNASG lt n gt where 1 lt n lt 9 and assigned Data Type C If the unassigned portion is greater than 99 characters the maximum length of a PEDSYS Item it is automatically divided into segments no longer than 99 characters with all segments assigned a numbered mnemonic UNASGI1 through UNASG9 Output Code File itemize cde will then contain descriptor records for each of these automatically created items making it possible for programs like REFORMAT etc to process itemize out even though it has not been put into its final PEDSYS format e Starting with an initial Code File A Code File may be named in response to the second request in the Initial Display shown above in which case ITEMIZE displays records with characters assigned to PEDSYS Data Items as specified by the Code File rather than as a string of unassigned characters There is no requirement that this Code File in fact fit the structure of the record but having an approximate pattern may be an efficient way to get started in determining the PEDSYS format of records in the file April 20 1999 ITEMIZE e 24 7 Once an input file has been selected the program examines the entire file to find the length of its longest record If the length of this record and record length as specified by the Code File are not the same the program uses by default the longer of the two as the length of the output record This leads to two possibilities a
34. The contents of this table are illustrated below the column of numbers on the left hand side of the panel have been added as a key to comments following and do not appear as part of the table itself 1 1 of the following items must be val ADA PHENO TYPE PEDTR 1 defined as invalid EQ 2 3 of the following items must be vali APOB Pvu2a GENO TYPE PEDTRTE 1 defined as invalid EQ CAI PHENO TYPE 3 defined as invalid EQ Unt EQ EQ G6PD PHENO TYPE 1 defined as invalid EQ Record 1 indicates that the single item to follow must be valid if Ego is to remain in a pedigree Record 2 starts with the mnemonics of the critical item here the mnemonics for the ADA pheno type followed by the name of the file from which data items are taken here PEDTRTEST XMP This pattern is repeated in records 6 9 and 14 Record 3 indicates the number of values defined explicitly as unacceptable for this item Record 4 the EQ operator by itself defines the default missing data criterion of exclusion a blank character designating missing data in this case Record5 indicates that two of the three following items must be valid if Ego is to remain in the pedi gree Records 6 8 repeat the pattern of Records 2 through 4 This sequence is repeated again in records 14 through 16 Record 10 specifies that three unacceptable values for this item are designated explicitly
35. an accompanying Code File is generated and saved on the disk as well Such a Code File is named lt progname gt cde CDE in MS DOS where lt progname gt is the name of the program that produces the output and cde is an extension that identifies the file as an output A 10 e APPENDIX A June 12 1999 Code File Some programs produce more than one Data Output File in which case file names are displayed on the screen when processing is done Examples are nomergel out and nomerge2 out which are produced in addition to merge out by the program MERGE b Error Files Several PEDSYS programs check for internal consistency of information in individual records or in pedigrees When found errors are usually displayed on the screen and saved in an output file Error Files may have one of two configurations The most common is a simple text file with the extension err consisting of records bearing an error message of varying length and format No accompanying Code File is provided PEDSYS programs that produce Error Files of this sort are AGE ANCESTOR COMBINE COUNTPED DATALINK DELRECS GENEFREO INDEX MAKEPED MERGE NEWITEM PREPDRAW SETDATA SETMASTR and SIBSHIP The other configuration is a PEDSYS file consisting of strictly formatted error messages and which has an accompanying Code File These files are named lt progname gt err out and lt progname gt err cde respectively where lt progname gt is a PEDSYS program name or its abbrevia
36. has the effect of directing ITEMIZE to check that pedigree data required in a Master File are present by searching for Standard Mnemonics EGO or ID BIRTH FA or SIRE MO or DAM and SEX An opportunity to assign Standard Mnemonics is provided if they are not found initially C Entry of C or default RETURN at this point begins the process of creating a PEDSYS Data File The parsing procedure described below is identical for both Data Files and Master Files since checking for Standard Mnemonics is not done until the record structure of the foreign file has been determined see the section on Checking for Standard Mnemonics below e Starting without an initial Code File As an example we will use ITEMIZE to determine the format of Example Master File records as can be seen from the file name entered in the display above We will assume for purposes of this example that no Code File exists for MASTER XMP An n has been entered in the display above indicating that the output is to conform to Master File specifications This is followed by the next display ER XMP Record 1 of 32 Length 95 0ID06119720309 M1998042 O1ID042 1 0 Enter A to ASSIGN first item R to display an alternate RECORD X to SAVE and EXIT gt a The Status Line appears at the top showing the file name number of the input record displayed below number of the last record in the input file record length and display page number Next t
37. is either the number of characters as yet unassigned to in the input record or 99 the maximum number of characters permitted in a PEDSYS Data Item The upper limit implies that an insertion may not be made if its width exceeds the number of unassigned characters remaining in the input record If an item of a certain width cannot be inserted because there are insufficient characters remaining it will be necessary to decrease the width or delete one or more items so as to accommodate the frame shift W Change WIDTH of Item Entering W lt n gt where lt n gt is a number corresponding to a previously entered item produces a request for a new width of the item Changing the width of an item shifts its right hand boundary in either direction by a number of characters equal to the difference between the new and old widths old minus new This change produces a downstream frame shift that is all item boundaries to the right of the modified item are also shifted left or right by the difference in old and new widths of the modified item Characters included in the unassigned portion of the record are shifted accordingly Limits on width are 1through lt unchars gt where lt unchars gt is either the number of characters as yet unassigned to in the input record or 99 the maximum number of characters permitted in a PEDSYS Data Item These limits imply that an item cannot be deleted by changing its width and that its width cannot be increased unless t
38. or Paul Mamelka paulm darwin sfbr org Department of Genetics Southwest Foundation for Biomedical Research P O Box 760549 San Antonio TX 78245 0549 Voice 210 674 1410 FAX 210 670 3317 Thanks The SFBR web site can be reached by pointing your browser to www sfbr org The same address may be used for anonymous FTP transfers Future PEDSYS updates will be posted here when available Fe F 8 INSTALLATION and SETUP Solaris 2 5 June 10 1999
39. or from the same list entered from the keyboard One member of which is selected from one file or list and the other member from a second file or list Enter number above corresponding to the source of pairs or Q to quit gt 1 1 Both members of pairs selected from the same source A 1 entered in the command line specifies that both members of the pair are to be selected from the same source This choice is followed by the following display from which the composition of selected pairs is specified opposite sex same sex etc Kinship coefficients may be calculated between individuals specified as All opposite sexed pairs All same sexed pairs All pairs regardless of sex Specified pairs of IDs Enter number corresponding to choice gt 1 e Options 1 3 Any of the first three options selected from the pair composition menu above results in a request for the source of pairs for which calculations will be made Here a 1 has been entered specifying that all opposite sexed pairs will be formed and analyzed Coefficients may be calculated for pairs entered from 1 Keyboard 2 Unlinked File 3 EXAMPLE 4 LOCUS Sub directory Enter number above corresponding to the appropriate source of pairs gt April 20 1999 KINSHIP 25 3 Proband IDs entered from the keyboard Prior to entry the form of the IDs Permanent or Sequential must be specified This is foll
40. sa Creating Records for Fictitious Offspring Only one fictitious offspring is created for a given pair no other checks for reciprocal mate refer ences are done Records created are then indexed with the rest of the file sa A note on the use of integers as Permanent IDs e PEDSYS Permanent IDs are normally in character format Data Type C and left justified This convention may be problematic if PIDs consist solely of integers that must sort in numerical order because the collating sequence for characters is different from that for integers It is strongly recommended that PIDs be kept as Data Type C and contain non integer characters preferably in the leading position to avoid confusion with Sequential IDs 22 8 e INDEX April 19 1999 Error Messages and Displays Because INDEX plays such an important part in the organization of pedigree databases considerable effort has gone into preventing errors from being incorporated into the data Protection from permanent damage is provided at three levels a Errors that affect single records or that lead to an incomplete pedigree structure are displayed on the console screen during program execution and are recorded in file index err The program produces output files and otherwise terminates normally b Most errors that lead to incorrect pedigree structure are displayed on the console screen during program execution and are recorded in file index err In addition these errors
41. to serve as passwords of individuals who are given write access that is who are authorized to make changes to the Data File using program ALTERDAT s There must be a separate Unlinked Data File Descriptor Record for each unlinked Data File specified in the Unlinked Data File Count Record Unlinked Data Files need not include an extension but they cannot be accessed by PEDSYS programs unless they have an accompanying Code File in the Data Directory named lt filename gt cde where lt filename gt is the same as the name of the Data File ignoring any extension t Maximum length of the Descriptor Record is 64 characters so that the directory path may be included as part of the file name 10 The Shell Menu Files a Sun Microsystems Unix Program PEDSYS reads four pairs of text files corresponding to the function groups described in Chapter General Data Management Programs menu A prog A File Management Programs menu B prog B Pedigree Management Programs menu C prog C Genetic Data Management Programs menu D prog D The program displays the contents of a menu file which contains a list of program names and descriptions and depending on the function selected from the keyboard calls the matching PEDSYS program listed in the accompanying prog file b MS DOS Batch file PEDSYS BAT calls program PEDSYSP EXE This program displays the contents of a file PEDMENU which contains a list of program names and descriptions Depending on the fu
42. usually a Permanent ID Sequential ID or Sample No etc gt 1 Here Ego PID has been selected as the identifier Although it is in the first position in the exam ple it need not be In the case of a Single entry Data File the identifier must be unique to each record and once it has been selected records are sorted by the identifier so that the file can be searched efficiently Commands E A and D Edit Add and Delete records in an unlinked Single entry Data File Once an identifier has been selected and the file is sorted ALTERDAT Edit Add and Delete func tions are virtually identical to those described above for Linked files Commands O F and L Edit controls for an unlinked Single entry Data File Setting order of access confirmation status and edit log for unlinked files is the same as that for Linked files Command N Create a new unlinked Single entry Data File Creation of a Single entry Data File that will not be linked to a Master File proceeds identically to the procedure described above for Linked files except a full file name with extension if there is one must be supplied before data entry begins Fi Unlinked Multiple entry Data Files In a Multiple entry Data File more than one record carries the same identifier ALTERDAT pre serves the original order of these records 4 12 e ALTERDAT April 20 1999 Commands E A and D Edit Add and Delete records in an unlinked Multiple entry Data File
43. 000 01 01 2000001 Two digit representation of year YY and YYMMDD is permitted as INPUT to DATES although it is not a legitimate PEDSYS date format and will result in an error message if encountered in input data to other PEDSYS programs DATES will not allow two digit representation of year in its OUTPUT Three digit representation of year YYY and YYYMMDD is permitted Calcul ations using three digit format assume that dates lie between A D 1200 and A D 2199 inclusive Four digit representation of year including YYYY and YYYYMMDD is always preferred Abbreviated month indicated by month code MON results in a three char acter representation i e 01 Jan 1991 Full alphabetic month speci fied by month code MONTH results in full spelling of the month name Gregorian and Julian forms may not be mixed except to the extent that representing the partial year as number of days since 1 January month code J may be thought of as Julian Year month and day may be separated by a period dash comma forward slash or a blank Any of these characters may be followed by a single additional blank Use of a separator is not required Simple conversion of date format is initiated by entering a number corre sponding to an item containing a date A constant number of years months or days may be added to or subtrac ted from a date by following the number corresponding to the date with a
44. 1 A new copy of DBFILES is created each time DBFILER is run 15 8 DBFILER May 27 1999 2 DBFILES OLD is created whenever DBFILER is run in a directory that already contains DBFILES 3 The DBFILER ADD function adds only file and sub directory names from DBFILES it does not create files or sub directories 4 Likewise the DBFILER DELETE function removes only file and sub directory names from DBFILES it does not delete files or sub directories 5 Records in DBFILES are added deleted and changed as the result of every program function 6 Records in DPOINT lt EXT gt are modified when ADD or DELETE functions are used with Linked Data Files 7 The contents or structure of Master Files or Data Files are not affected by DBFILER The only operations permitted with a newly created or empty DBFILES that is one in which the number of Master Files is 0 are to ADD a Master File unlinked Data File or sub directory A Data File may be added only after an existing Master File has been added When adding the first Data File a Data Pointer File will be created if it does not already exist However at this stage DPOINT lt EXT gt will be incomplete until program DATALINK has been run to establish pointers Only one new file may be specified as a Linked Data File in a single session or DBFILER Additional Linked Data Files may be specified only after the previous one has been linked using program DATALINK Although the number of
45. 19 1999 MAKEPED e 27 3 Choice 2 3 or 4 Proband IDs read from a Proband Input File A proband file is often a subset of the input pedigree file typically a Master File but may be any Data File whose records contain IDs in the appropriate form that is Permanent or Sequential Selection of a single item containing the proband ID is made from a Standard Item List Display EGO Permanent ID Sex M F or U EDIGREE NUMBE Birth Date YYYYM Exit Date YYYYMMDD ENERATION NU Sire s Permanent I Exit Code Dam s Permanent ID ate s Permanent ID ED Identify PROBAND File subset out Enter a number above corresponding to Proband ID or C to continue to next step gt 8 Here the pedigrees of the mates of individuals found in file subset out have been specified and the program proceeds to selection generational depth etc Method 2 Method 2 begins with the following sequence Enter P if probands are identified by Permanent ID S if by Sequential ID Enter number of steps in assembly of family units 1 6 or enter H for an explanation of the process gt 1 Enter proband s Permanent ID gt ID065 lt ID First the form of the IDs Permanent or Sequential used to identify pedigree members must be specified This is followed by a request for the number of steps to extend the pedigree outward from the proband and then fo
46. 26 25 24 23 22 21 20 19 0 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 IDO4 1982 1983 1984 1985 1986 01 21 1987 01 14 04 29 1988 03 08 5 06 1 05 1 03 1989 01 25 1990 01 03 1991 05 15 1992 05 01 1993 04 29 1994 04 08 Eo Fs OE Re Be Ra ea Ae me WWP db HO 01 Wi ODS Bo o N Oo N a OO O OO JE WOO NNNNNNNNNNNNN Enter lt n gt or lt n gt for new page PID S lt n gt 1 32 or lt n gt 1 96 to set top row gt or lt lt n gt to shift window I lt n gt 1 9 to set window L to lock columns O to change order to switch files N for new file H for help Q to quit gt Note that the individual ID042 displayed in the previously selected file SAMPLES XMP is the one shown when the switch to the new file occurs If there is no entry for an individual in the new file however the following message will appear April 19 1999 SHOWDATA e 41 3 No record for lt PID gt in lt filename gt Enter RETURN for the first record of this file or for next file At this point entry of an asterisk skips to the next file selected for display showing a a single record if the next file is a Master File or Single entry Data File or b multiple records if the new file is a Multiple entry Data File gt lt i gt or lt lt i gt where lt i gt is a number of items to be shifted in the range shown on the display Entry of this s
47. 988 08 31 986 12 15 989 10 12 994 09 23 996 07 27 993 03 18 996 09 08 996 10 13 974 03 30 978 12 21 978 12 31 979 04 04 982 06 01 987 06 26 985 08 14 992 09 27 991 09 08 997 11 30 1 32 or lt n gt 1 32 to set top row gt switch files N for new file F to find H for help 14 SIRE ID080 ID095 ID109 ID109 ID124 15 DAM UO peri cal UO oO ea Lo O1 O1 UT J J O1 ND OS N ID083 ID097 ID103 ID111 ID113 16 17 SEX EXIT 1998 04 20 1996 12 23 1996 11 14 1ZZRHUIEEZEE 1998 01 16 La g Hj Hj Hj zg 1998 01 18 1997 01 23 HSA AWS SSyyyys nz 1997 12 31 or lt lt n gt to shift window Q to quit 18 EXCODE puo arr a oor oe hHOOOOOOOMOOOOO I lt n gt 19 MATE D04 D06 D04 D03 DOS D06 D04 DO A R UO OO oO BADOO Ww OUWNUUDSLJUAONAN DI I od Files Input Any Master File or Data File and an associated Code File Output Console screen sa 8 8 BROWSE April 19 1999 April 19 1999 BROWSE 8 9 CALC Program CALC generates simple functions natural and base 10 logarithms and exponentiation of numerical variables kept on individual records and or will add to each record new items consisting of a an integer corresponding to the order of the record in the file b a randomly generated fraction from a uniform distribution between 0 0 and 1 0 c
48. AGE 3 5 be used to start this program Example age subset out Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file age out may be used as input to program AGE Output age out contains all records in the input file in their original order records contain all items in the input records in their original order followed by items containing age calculations age cde defines the record structure of age out age err identifies invalid dates and the records on which they appear Progam limits 12 output items That is up to 12 age calculations that result in single items years month or days or up to four age calculations that result in three items years months days etc sa 3 6 AGE June 12 1999 ALTERDAT ALTERDAT is a data entry and editing program for Data File records PEDSYS records are very simply formatted and can in principle be edited with any general purpose text editor However this is not recommended because of the danger of disrupting the fixed format of PEDSYS record structure Introductory Display EDSYS program ALTERDAT Copyright 1992 1999 SFBR ALTERDAT is a data entry and editing program used to modify or create Single or Multiple entry Data Files Two update Modes are available Interactive Mod items ar ntered or updated directly from the key board DATALINK must be run after creating Linked Data Files
49. Code File see below e Items 13 17 See date specifications in Data Types section above e Item 17 Because Exit Dates are not available for some populations this is not a required item in the Master File Nonetheless its inclusion is strongly advised and must follow specifications as listed in the table below June 12 1999 APPENDIX A e A 5 Item No Length m name nemonic Sequential ID SEQ her s SEQ FSEQ or SSI her s SEQ SEQ or DSI st Offspring SEQ KID1 t Paternal Sib SI PSIB Maternal Sib SI SIB t Full Sib SEQ FSIB Number of Offspring NKID Paternal Sibship Size PSIBSZ aternal Sibship Size SIBSZ Full Sibship Size FSIBSZ Ego Permanent ID EGO Birth Date Yr Mo Da Father s Perm ID other s Perm ID Sex M F U or 1 2 3 Exit Date Yr Mo Da Exit Code Pedigree ID Number Generation Number I oO OB WN FE 5 5 5 5 5 t D E 5 3 3 3 3 HHAQOQQQUQOMHMHHHHHHH A HW OO OANA OB W Nerrrrrre RAR RE I L LR A A position not fixed Eight digit dates preferred Optional e Item 18 The need to specify cause of exit may vary depending on the population in question In some studies it may be sufficient to distinguish the living from the dead which in some cases can be signified by the presence or absence of an Exit Date with no Exit Code needed or by a simple binary Exit Code i e A for alive D for dead alone or in combination with an
50. D1S1656 Genotypes 4 D2S1329 Genotypes GENEFREQ Select loci File merge out Enter numbers corresponding to loci for which gene and genotype frequencies are to be calculated or C to continue gt Here three loci have been chosen GENEFREQ makes two initial assumptions about genetic loci First it assumes that data are phenotypic unless one of the last three mnemonic words associated with the Code File entry for a locus is GENO or G TYPE in which case the data are interpreted as geno ypic Second the program assumes that phenotypes are autosomal codominant and follow conventions listed in Appendix C Rules for Genotype and Phenotype Nomenclature unless specified otherwise in a Genotype Phenotype Map File GENOMAP lt EXT gt see Appendix A Definitions Data and File Types GENEFREO first searches the Data Directory for map file GENOMAP lt EXT gt If the file is not found or if the selected phenotype is not included in it the following display appears o entries for selected loci found in GENOMAP XMP Enter RETURN if all loci are autosomal co dominant Otherwis nter name of alternate genotype phenotype map file loci not listed in a map file are assumed to be autosomal co dominant 5 A Phenotype Genotype Map is not required for autosomal codominant loci that adhere to the con ventions listed in Appendix C Presence of a map file eliminates the need for the t
51. Data File lt filename gt lt EXT gt is the updated Data File from which records have been deleted lt filename gt OLD is a backup copy of the Data File as it was before deletions were made lt filename gt ODE is a backup copy of lt filename gt DEL delrecs err contains a record and diagnosis of deletions that were attempted but were unsuc cessfully completed because of an error or inconsistency detected by the program Program Limits Records for a maximum of 250 individuals may be deleted at one time Fa April 20 1999 DELRECS e 16 3 16 4 DELRECS April 20 1999 IDOWNCODE DOWNCODE simplifies the genotypic structure of a locus by combining selected alleles into a single type The program iteratively combines pairs of alleles and evaluates loss of information about parental origins of each allele Analysis is limited to autosomal codominant loci only Introductory Displays EDSYS program DOWNCODE Copyright 1994 1999 SFBR DOWNCODE simplifies the genotypic structure of a locus by combining selected alleles into a single type 1 Unlinked File 2 merge out 3 EXAMPLE 4 LOCUS Sub directory Enter number file name or Q to quit gt Loci may be selected for analysis from linked or unlinked files containing genotypes or phenotypes for one or more loci When a Linked Data File containing genotypic or phenotypic data has been selec ted DOWNCODE proceeds directly to
52. Exit Date In other cases a lost to follow up code may be needed while in others Exit Codes may specify detailed causes of death etc See Dyke and Mamelka 1989 for a demographic analysis package that uses this coding scheme A set of standardized Exit Codes has been proposed for nonhuman primate populations Dyke 1993 In any case Exit Codes are optional and may be defined arbitrarily e Items 19 and 20 Pedigree Identification Number and Generation Number are added automatically to Master File records by program INDEX e signifies that a Master File may contain additional items e Many pedigree analysis programs require that records of parents appear before those of their off spring in population files This order is automatically enforced when producing Master Files with program INDEX or the ALTMASTR SETMASTR sequence 3 Data Files PEDSYS uses Data Files for storage of information not kept in the Master File PEDSYS programs assume that for each individual represented in a Data File there is a corresponding entry in the Master File to which it is formally linked but not vice versa that is there need not be Data File entries for all individuals in a Master File There are two types of Data Files a Single entry Data Files contain items for which a single value is recorded for each individual birth weight age at first mating etc These files may be created and manipulated with many A 6 APPENDIX A June 12 1999
53. FSEQ or SSEQ and MSEQ or DSEQ a pedigree file con taining this information along with Ego PIDs that match those in the input file must be selected Pedigree information is not present in file P Enter I to select IDs from this file P to select a PEDIGREE file R to RESELECT data file Q to QUIT program 32 2 e PEDTRIM July 8 1999 2 Selecting data for analysis a Specifying Critical Data Items Some data selected for inclusion in output may play little or no role in determining whether an in dividual is trimmed from the pedigree for example an occasional missing covariate such as age or sex code may not be a serious loss for some analyses making removal of such individuals unwarranted Other data however may be more critical to an analysis such that its absence may make Ego a candi date for removal this is typically the case for genetic marker or phenotype data that is the primary object of analysis PEDTRIM requires that a list of critical data items and their unacceptable values be kept as a table Instructions appearing in the next display control the source of this table Critical data items and their specifications are kept as a table stored in file pedtrim tab Enter S to START a new Pedtrim Table from the keyboard U to USE a previously created Pedtrim Table Q to QUIT program without executing PEDTRIM creates a default table file named pedtrim tab
54. Fields in LINKAGE record format are space delimited Alleles of genotypic fields are also space delimited LINKAGE Error Messages and Displays TRANSLAT detects a number of data conditions that force program LINKAGE to terminate without execution When any of these conditions is encountered TRANSLAT writes error messages to file translat err These messages are lt ego gt One parent missing lt ego gt No parents and no offspring lt ego gt Affection Status not 0 1 or 2 lt ego gt Sex code not 1 or 2 lt ego gt Parent not included in file as Ego 45 10 e TRANSLAT May 19 1999 11 PEDSYS to SOLAR MIXED format SOLAR MIXED is an interim variance component analysis that requires preprocessing of PEDSYS data Pedigree Number PEDNO and IBD index IBDID are required and SEX must be expressed as 0 1 or 2 for U M and F respectively If mnemonic IBDID is not found in the input Code File the following display appears from which an item may be selected to represent this variable Here Item 11 EGO SEQUENTIAL ID has been chosen ENTIAL ID EGO Permanent ID Sire s Permanent ID Dam s Permanent ID Sex M F or U PEDIGREE NUMBER 6 ADA Phenotype 7 APOB Pvu2a Genotype 8 Tot Ser Cholesterol 9 APOAI Level 10 Discrete Trait TRANSLAT Select IBDID RANSTEST XMP gt 11 Enter number corresponding to IBDID Next one or mor
55. File MPOINT lt EXT gt 4 Data Files are linked to a Master File by a Data Pointer File DPOINT lt EXT gt 5 Records of multiple entry Data Files must be linked by internal pointers Although these principles are simple their implementation must be precise Of all file manage ment procedures perhaps none is as critical as the initial creation of a PEDSYS database A major effort has gone into developing programs that automate this and other file management operations The instructions that follow for creating PEDSYS files assume a That PEDSYS program files and auxiliary files CODE STD and DEVICES have been installed in the PEDSYS Program Directory and that The appropriate system files have been modified to include a path to the PEDSYS Program Directory b That a file extension that identifies the population as well as appropriate labels and file names have been chosen and that Master File Data File Pointer File etc names are in upper case see Appendix A c That a PEDSYS Data Directory has been created This directory may initially contain the Directory File DBFILES although this file will be created automatically by programs ALTMASTR or ALTERDAT if it is not found in the directory Fe Creating a Master File from the Keyboard In addition to the initial assumptions above creation of a Master File by entering data from the keyboard assumes that pedigree data are available in the form of paper records with a s
56. File Count Record i Key j c Map 0000000000000000000000000000000000000000000000000000000000000000 Start 1 4 Format I3 Records 4 6 Linked Data File Descriptor Record s k Key Start 1 40 43 45 Format A3 1X A8 1X A25 1X 12 1X 2 Al 1X 5X 4A4 Record 7 Unlinked Data File Count Record r Key j c Map 0000000000000000000000000000000000000000000000000000000000000000 Start 1 4 Format I3 Record 8 Unlinked Data File Descriptor Record s Where represents a character in a field read by PEDSYS programs o represents a single blank ignored by PEDSYS programs often used as a visual separator is a visual marker pointing to the first character in each field Numbers below the vertical markers represent the starting column of each field June 12 1999 APPENDIX A A 13 e Notes on DBFILES Record Formats a The Master File Count Record is always the first record in DBFILES Maximum length of this and all records in DBFILES is 67 characters b The first field processed in this record is an integer in columns 1 3 indicating the number of Master Files included in the Data Directory see Chapter II SETUP and INSTALLATION The maximum number of Master Files per directory is 5 but in most cases we have found it advantageous to keep a single Master File and its associated Data Files in a separate directory or subdirectory c It is often useful to include a note her
57. File interactively without an intermediate step 4 4 Creating a Pedigree Database 10 December 1996 Step 3 Run a spot check of records in lt FILENAME gt lt EXT gt using program BROWSE or SHOW If data on the records appear to be correct go on to Step 4 If data are not correct it may be necessary to edit records using program ALTERDAT Step 4 Run program DBFILER in ADD Mode choosing option D to add a linked Data File and entering the number corresponding to the Master File to which the Data File is to be linked and the name of the Data File itself when prompted DBFILER will modify the Directory File DBFILES and create or modify as necessary a Data Pointer File DPOINT lt EXT gt so that each is appropriately configured for use as input to program DATALINK Step 5 Run program DATALINK entering the number corresponding to the Master File to which the Data File is to be linked when prompted DATALINK produces an updated version of DPOINT lt EXT gt that contains the appropriate pointers between the Master File and Data Files DATALINK also generates a new version of lt FILENAME gt lt EXT gt with updated internal pointers if it is a Multiple entry Data File see File Types in Appendix A Output file datalink err may reveal inconsistencies that require correcting the original data see documentation for program ALTERDAT Fe Creating a Linked Data File from Imported Computer readable Data Creation of a Linked Data File
58. File records Entering E EDIT results in a Standard Item List as shown below from which items to be modified are selected so that only those that must be changed will appear on the Edit screen 4 2 ALTERDAT April 20 1999 1 ADA Phenotype 3 Tot Ser Cholestero 2 APOB Pvu2a Genotype H 4 APOAI Level ALTERDAT Items to be modified File QUANTGEN XMP Enter numbers corresponding to items to be modified Precede number with H to carry over entry of item from one record to the next Enter A or HA to include all items C to continue to next step gt Preceding numbers with an H for hold carries over the previously entered value to the next record to be changed or added This feature makes it unnecessary to re enter duplicate values on suc cessive records The value displayed in the space provided for the item on the data entry screen will be added to the record unless it is changed or erased The new change or erasure will then be passed to sub sequent records selected for alteration or addition In the example above all items have been selected for modification and the APOAI Level phenotype has been marked for hold over After the usual confirmation step a request appears for the Permanent ID associated with the record to be changed Last entry in QUANTGEN XMP is ID077 EDIT Record Random Order Enter individual s Permanent ID or RETURN to change mode of entry gt ID069 lt EG
59. Linked Data File The following errors may be reported if this condition is not met the number of each error appears in parentheses at the end of the error record April 20 1999 DELRECS e 16 1 lt ego gt Record in lt FILENAME gt lt EXT gt not deleted EGO not found in lt ego gt Record found in lt FILENAME gt lt EXT gt that is not in Master File o N bp where lt ego gt refers to EGO s PID as it was entered in the DELETE lt EXT gt or lt FILENAME gt DEL file and MF is an abbreviation for Master File The usual cause of error 1 is an attempt to delete from a Data File that is incorrectly linked to the Master File To correct the error run program DATALINK Error 2 is a generalized linkage error that occurs when attempting to establish pointers to incorrectly created Data Files See notes for program DATALINK for suggested corrections z Unlinked Files If records identified by PID or other identifier and record number in file lt filename gt DEL are not found in an unlinked Data File the following error will be reported lt ID gt found in lt filename gt DEL not in record lt n gt of lt filename gt lt ext gt 03 The usual cause of error 3 is a change in the unlinked Data File since the creation of the file containing PIDs of records to be deleted lt filename gt DEL To correct this error either run DELRECS with the original Data File or ge
60. Linked Files Entry of choice 3 above results in the following Secondary File List from which up to five linked files may be selected Linked files i Example Master File E Zia arkers Quant P types Blood Sample Inventory Hemoglobin Levels lore than one LINKED file may be selected for repeated sequential display Enter numbers corresponding to file s above in the order they are to b shown Enter RETURN alone to continue to next step gt 1 Here the Example Master File and the Markers Quant P types file have been marked with an asterisk indicating that they have been selected for display The order of selection and display is usually not critical since switching between files is cyclical However the Master File is frequently chosen first Entry of RETURN alone results in a display of the first individual in the file The display below shows the record for individual ID061 April 19 1999 SHOW 40 1 ID IDO61 File MAST Record 1 32 ta Q SIRE EGO SEQUENTIAL ID SIRE S SEQ DAM S SEQ FIRST OFFSPRING SEQ PATERNAL SIB SI MATERNAL SIB SI FULL SIB SEQ ER OF OFFSPRING ERNAL SIBSHIP SIZE ERNAL SIBSHIP SIZE L SIBSHIP SIZE 0 EGO Permanent ID IDO61 Birth Date YYYYM 1972 03 09 Sire s Permanent I Dam s Permanent ID Sex M F or U M Exit Date YYYYMMD 1998 04 20 Exit Code 1 ate s Permanent ID042 PEDIGREE NUMBER dL GENERATION NUMBER 0
61. Linked or Unlinked Data Files in the current directory The maximum number of Linked Data Files per Master File is 50 k There must be a separate Linked Data File Descriptor Record for each Linked Data File specified in the Linked Data File Count Record Total length is 67 characters 1 This field columns 5 12 contains a Data File name without its extension MARKERS and SAMPLES in the example The extension described in e above is appended to this name when the files are accessed by PEDSYS programs m This field columns 14 38 contains a label that identifies the Data File for screen and print displays The Example Marker Phenotypes and Blood Inventory files are given in the example above n The number contained in this field columns 40 41 refers to the position of the data pointer in Data Pointer File records not counting Ego s Sequential ID which always appears in the first position See 6 The Data Pointer File above A 14 e APPENDIX A June 12 1999 o This field column 43 contains a logical variable specifying whether the Data File is a Multiple entry file having internal pointers T yes F no p This field column 45 contains a logical variable specifying the default status of the Log File generated by program ALTERDAT T Log normally on F Log normally off This default may be overridden when running ALTERDAT q Four four character strings may be entered here columns 52 55 56 59 60 63 and 64 67
62. Macintosh point and click convenience to the text based interface of the applications mouse clicks on the application display window may be used to enter a character or a RETURN at the prompt line Clicking on a screen character is the same as typing it at the keyboard while clicking an empty space is the equivalent of pressing the RETURN key For example in order to enter the standard Quit code click on the Q shown in the display and then on any empty screen space This works only if the mouse cursor is clicked and released within the same character space If the mouse is moved before the button is released the character or RETURN will not be entered Currently only one character may be entered at a time this way and only characters that are visible on the screen This feature may be elaborated upon in future editions perhaps with support for a simple Copy amp Paste approach to entering filenames Fe June 10 1999 INSTALLATION and SETUP Macintosh OS F 7 Comments If you have comments or problem descriptions to forward please fill out this page and mail to the address below or send as e mail if preferred Name Address E mail Phone System Configuration MacOS version number Machine model Memory capacity Disk storage available Printers in use Special software in use Problem Description or Comments Please send the report to Bennett Dyke bdyke darwin sfbr org
63. Note to edit Sub directory Note to return to initial function menu Here the sub directory note has been selected for change RETURN produces the following dis play EDIT Sub directory Note Enter new note one or more blanks to remove note or RETURN to continue without changing gt Sub directories 1999 02 15 Here we have added a date to the original note Sub directories making it Sub directories 1999 02 15 Fa V VIEW Command V displays the current contents of DBFILES 15 6 DBFILER May 27 1999 BFILE Master Files Example Master File Linked Data Files UANTGE arkers Quant P types Blood Sample Inventory Hemoglobin Levels w fil xampl Data Files WEIGHTS X 1 Sub directories 1999 02 15 LOCUS Press RETURN to continue gt This display shows the effects on the XMP Directory File of previous example operations described above the password added in to the Master File the EDIT sequence can be seen in line 2 the descriptor record for new Linked Data File NEWDATA XMP can be seen in line 7 addition of the date to the sub directory note appears in line 7 Comparing this example with the original DBFILES shows also that the new Linked Data File has been assigned to position 4 in the Data Pointer File DPOINT XMP and that the Data Fil
64. P types has been selected in the example above This is followed by a request for entry of a password if passwords have been included in the Data File Descriptor Record of DBFILES see note q in the Notes on DBFILES Record Formats section in Appendix A After a correct password has been entered or if no password is required the following instruction appears Updating QUANTGEN XMP Interactive Mode Make a backup copy of QUANTGEN XMP before making changes Y N gt If the Backup option has been chosen the contents of lt FILENAME gt lt EXT gt will be copied and saved as lt FILENAME gt OLD In the example above the Data File selected was QUANTGEN XMP and the backup file will be named QUANTGEN OLD ALTERDAT begins its data entry cycle for modification of a linked Single entry Data File with the following options display Updating QUANTGEN XMP Interactive Mode Enter E to EDIT records A to ADD records D to DELETE records Edit control O set Order of access Order is RANDOM F set conFirmation display Confirmation is ON L to switch Log setting LOG is ON If finished with QUANTGEN XMP C to CHANGE existing file N to start a NEW file Q to QUIT program The first three commands shown in this display govern the type of modification that will be done to the file selected editing adding or deleting records Command E Edit Linked Single entry Data
65. Parameters specified for NUMBER OF OFFSPRING by SEX in the Example Master File April 19 1999 TALLY e 44 3 export home population bdyke example MASTER XMP DISTRIBUTION PARAMETERS FOR NUMBER OF OFFSPRING BY Sex M F or U Sex M F or U MEAN VAR STDV LOW HIGH SKEWNESS KURTOSIS SUM N 1 0588 1 0588 1 0290 0 0000 4 0000 1 1882 1 3796 18 0000 17 1 2000 0 6000 0 7746 0 0000 3 0000 0 5508 0 0578 18 0000 15 se Output control Tabular output is always sent to file tally tab but may also be sent directly to one or more printers depending on the hardware available or the console screen Output from TALLY is written to file tally tab but also can be sent directly to the following output devices 1 Main Lab LaserWriterII 2 Main Lab Line Printer Printer Room Sun LaserWriter 4 Console Screen Enter number of device or C to continue without printing gt In addition to output sent to file tally tab results of computations can be output in PEDSYS format and sent to files tally lt n gt out and tally lt n gt cde where lt n gt is the order that variables are selected for computation This is especially valuable when tabulating values across individuals identified by EGO PID which makes it possible to use the file as a PEDSYS unlinked Data File PEDSYS formatted output is controlled by the following sequence In addition to output sent to file tally t
66. Phenotype Mapping Record is repeated for each of the n unique combinations of allele pairs disregarding parental origin No Na Na 1 2 for autosomal loci ne Ng na 3 2 for X linked loci 1 The first two fields of this record consist of a pair of allele labels from the list described in g above m One of the next np fields contains a if the phenotype found in the corresponding position in the Phenotype Label Record is produced by the allele pair Remaining fields contain a blank e Loci having any mode of inheritance may be listed in the Genotype Phenotype Map File but inclusion is required only if they are phenotypes that are X linked and or exhibit dominance Inclusion of autosomal codominant loci is necessary only if a distinction is to be made between allele and phenotype symbols lower vs upper case for example 14 Temporary System Files Several PEDSYS programs create one or more files with the extension tmp or uppercase TMP which are used to save data during program execution and which are erased upon successful completion of the task The tmp extension is reserved for PEDSYS system use and should not be used in naming Master Files or Data Files In addition some PEDSYS programs that direct their output to disk files use tmp files as input to programs run subsequently These files contain information that helps keep track of prior manipulations performed on a data set The files are LASTFILE TMP Which
67. Ratio NKID FSIBSZ SE KidSib Ratio EWIT EM Conversion Table newitem tab A to Al D to D Q to Q E to ELE UIT CO INU Enter Number of table entry above to EDIT DD an entry to end of list E an entry program with option to save Conversion Table E Save table execute program Entry of a number corresponding to one of the Conversion Table entries here entry 3 results in the following EDIT screen display April 19 1999 NEWITEM 29 3 EGO SEQUENTIAL ID 9 PATERNAL SIBSHIP SIZ Exi Date YYYYMMDD SIRE S S 10 MATERNAL SIBSHIP SIZ Exi Code DAM S SE 11 FULL SIBSHIP SIZI s Permanent ID FIRST OFFSPRING SEQ 12 EGO Permanent ID EDIGREE NUMBER NEXT PATERNAL SIB SI 13 Birth Date YYYYMMDD ENERATION NU NEXT MATERNAL SIB SI 14 Sire s Permanent ID Kids Sibs Ratio NEXT FULL SIB SEQ 15 Dam s Permanent ID NUMBER OF OFFSPRING 16 Sex M F or U I oO UO FWN E EWITEM EDIT Conversion Table newitem tab R nter Item Number Operator Test Value sequence to right of pointer gt Enter one or more spaces to remove sequence enter RETURN alone to advance to next sequence to go to next step Last entry gt 16 EQ TUS Here the third Conversion Table entry
68. The display below shows the first screen page of the Example Master File BROWSE starts initially with the first item of the first record in the upper left corner of the data display window The display window extends to the right for as many additional complete items as will fit on the screen typically 80 characters wide and downward as many records as will fill the screen see Notes below Columns are unlocked April 19 1999 BROWSE e 8 1 ER XMP Items 21 Top record 1 32 1 2 3 4 5 6 7 8 9 10 11 12 SEO SSE DSEQ KID1 PSIB MSIB FSIB NKID PSIBSZ MSIBSZ FSIBSZ ID IDO61 ID056 1D038 1D042 ID066 IDO55 ID062 1D045 IDO19 ID063 ID047 ID065 ID034 IDO15 ID068 J oO OF WN E N OO 0 O O ws m ie 10 17 15 14 N H 12 11 11 DS ODP O OO O O OO O O_O 6e BOO O O OO O0 O NN _Fr_r tropo NN NADE OOO OGO OLO NINE_HrErYtYH oO 0 9 0 20 2 20200 PR RoR 58 OS Oo OS E N H H H N H H H H H H H N wo a ba a ou Oo O ba H HN 3 2 i 6 7 7 Enter lt n gt or lt n gt for new page PID S lt n gt 1 32 or lt n gt 1 32 to set top row gt or lt lt n gt to shift window I lt n gt 1 21 to set window L to lock columns to switch files N for new file F to find H for help Q to quit gt Commands lt n gt lt n gt Entry of or displays a new screen
69. XMP and Q formats in CODE XMP and QUANTG E select Key I UANTGEN XMP do not have the same format EN CD For Enter Q to quit program April 19 1999 If re selection of Key Items is chosen the program returns to the Item List Display shown above The Merge Key may be made up of more than one Data Item in which case the confirmation display appears as follows Merge will be based on MASTER XMP TARGET file FIRST OFFSPRING SEQ Sex M F or U MASTER XMP DONOR file EGO SEQUENTIAL ID Sex U Is this correct gt This example also shows that it is possible for the same file to be both Target and Donor This particular merge produces records containing information about parents and their same sexed first off spring on the same record Note also that the Donor file need not be a Linked Data File records from any two files may be merged so long as they have the same Key Item format see Selecting Key Items below If the Donor file is not linked as in the example displayed below the following query appears Does examped DONOR file contain more than one record for the same Key Item s Y N gt If the answer is Y the following message is displayed WARNING There should be only one record in examped DONOR file for each key in MASTER XMP otherwise the record selected for merging is unpredictable Switching orde
70. Y directs SUBSET to treat numerical fields filled with blanks as a single 0 or 0 following FORTRAN integer and floating point format conventions This interpretation applies to all blank entries made at the keyboard for comparison with numerical items as well as blank numerical items read from records in the input file Once chosen this option applies to all 43 2 e SUBSET April 20 1999 numerical items it is not possible for example to interpret blanks as zeros in one numerical field and not in another Responding with N directs SUBSET to honor blanks as legitimate characters in their own right ASCII Code 32 that are quite different from the zero character ASCII Code 48 This setting makes it possible for example to distinguish and eliminate unwanted blank entries in numerical items e A final request always appears before SUBSET begins its execution INCLUDED records will be saved in subset out Save EXCLUDED records in nosubset out Y N gt Entering Y directs SUBSET to save separately records that do not meet the criteria for inclusion in the subset Entering N directs SUBSET to skip excluded records Notes e The substring feature permits a sequence of characters occurring at any position in the field occupied by the item to be compared with the sequence entered at the keyboard For example the command in 13 eq 1966 would create a subset that included all individuals born in that year regardl
71. a Sequential ID s lt n gt for an individual not in the Data File produces the following message No record for sequential number s lt n gt in lt filename gt momentarily after which the display reverts unchanged to the previously selected record 40 2 e SHOW April 19 1999 lt n gt where lt n gt is a pointer that is the position of a particular record in the file lt n gt must be in the range 1 through lt nrecs gt In the example above the counter on the status line of the display reads Record 10 20 so that lt nrecs gt 20 and 1 lt lt n gt lt 20 The command makes it possible to specify the display of records in a Data File independently of the Sequential ID and thus is also appropriate for use with Unlinked Data Files Note that used with a Master File it produces the same result as the S command lt N gt lt n gt Entry of or followed by an integer and RETURN advances through the file W containing EGO s records by steps displaying a new set of individuals lt n gt records from the current record For example if record 1 is displayed on the screen entry of 4 would result in the display of record 5 The default value of lt n gt is 1 so that entry of RETURN alone advances the display by one record This command like the command permits specification of records independently of the Sequential ID making it appropriate for use with Unlinked Data Files This command locks rows in a man
72. an item number with U u results in the following display from which constants for con version between selected conventional measurements and Syst me International D Unit s standard units SI Units may be chosen Converted items are added to the end of each record For example 9 2 e CALC April 19 1999 entry of u4 in the command line shown in the Item List Display of the QUANTGEN XMP file below specifies conversion of Total serum Cholesterol measurements Item 4 from mg dl to SI Units 1 Ego ID 3 APOB Pvu2a Genotype 5 APOAI Level 2 ADA Phenotype 4 Tot Ser Cholestero File QUANTGEN XMP CALC Simple calculations sequences Enter first operand from the list above or a constant preceded by K operator E then a second operand Precede operand with Log or LN for logs U for SI Unit conversion Enter R for random fractions S for integer sequence H for help C to continue to next step gt u4 lt COMMAND Entry of RETURN produces the following display from which the appropriate conversion factor may be chosen Convert Tot Ser Cholesterol System Input Units SI Units Conversion Constant Calories kcal kJ 1868 Cholesterol mg dl mmol 1 02586 Glucose mg dl mmol 1 05551 Insulin uU ml pmol 1 00000 Triglycerides mg dl mmol 1 01143 Enter number above corresponding to system to be converted TO SI units Precede number by R to convert FROM S
73. an opportunity to modify the Symbol Selection Table Ent to VIEW and EDIT text and symbol selections to IDENTIFY pedigree records for inclusion in output file to SAVE file prepdraw tab and EXIT program to QUIT program without executing or saving table r letter abov corresponding to action to be taken gt Command V displays the Symbol Selection Table Edit Display Palette 1 IF EXCODE IF EGO EQ Palette 2 IF TSC G IF TSC G Palette 3 IF APOAI Palette 4 IF ADA PHENO TYPE EQ 1 IDO15 SYMBOL SYMBOL Deceased Proband KO AND K99 THI SC K99 EN SYMBOI HEN SYMBOL Trait 144 Li EQ KO EN SY evel OL EQ BLANKS TH EN SYMBOL Trait 2 3 Asterisk Gray fill Add delete entries EPDRAW File prepdraw tab Enter D to DE LE A to ADD C to CO E an entry a symbol from palettes INUE Du Option D produces a request for one or more numbers corresponding to text and or symbol selection com mands in the display above When numbers are entered corresponding lines are deleted A returns the palette selection display from which new symbols or attributes may be select ed P produces of subsequent pages of the table C is entered when the Symbol Selection Table requires no further modification Ma
74. and commands are the same as in Choice 1 Fa April 19 1999 INDEX e 22 3 Choice 3 Index of EGO FA and MO without producing Master File Choice 3 automatically indexes EGO FA and MO but does not generate derived items 4 11 Pedi gree Identification Numbers or Generation Numbers normally included in Master File records and a Master Pointer File is not generated When this mode is selected a modified File List appears from which a pedigree file may be chosen When an appropriate pedigree file and its Code File have been entered the following screen is shown EGO SEQUENTIAL ID Sire s Permanent ID 11 Mate s Permanent ID SIRE S SEQ Dam s Permanent ID 12 PEDIGREE NUMBER DAM S SEQ Sex M F or U 13 GENERATION NUMBER EGO Permanent ID Exit Date YYYYMMDD Birth Date YYYYMMDD Exit Code INDEX Items to be included File examped Enter numbers corresponding to items shown above in the order they are to be included in indexed record Enter A to list all items shown above C to continue to next step gt EGO FA and MO are pre selected for indexing and only their Sequential IDs will be included in the output file unless other items are selected at this point Subsequent queries and commands are the same as in Choice 1 If the input file is in Master File format Item List Display contains the following warning
75. appropriate Code File has b When a file has been selected the following Item List Display appears EGO SEQ ENTIAL ID SIRE S S DAM S SI EO FIRST OFFSPRING SEQ PA ERNAL SIB SI 8 9 10 EL 12 U 15 ER OF OFFSPRING PATERNAL SIBSHIP SIZ IATERNAL SIBSHIP SIZ FULL SIBSHIP SIZI EGO Permanent ID T9 MA ERNAL SIB SI 1 SIB SEQ 13 14 20 21 Birth Date YYYYMMD Sire s Permanent ID 17 1 18 I Dam s Permanent ID Sex M F or U it Date YYYYMMDD it Code ate s Permanent ID EDIGREE NUMBER ENERATION NU SUBSI File MASTER X Enter operator IN or EX value each precede 2nd in quotes in 16 eq M gt and 20 gt 0 item number separated by blanks Precede operator with to compare i line with AND or OR for compound comparison Enter H for help relational EQ N and E GT GE LT or LE C to begin subset tems Enclose substrings The display above shows commands entered to generate a subset of the Example Master File that would include all males in 16 eq M that are in generation 1 or higher and 20 gt 0 Notes on query logic e To compare a listed item with a numerical or alphabetic value enter commands separated by a single blank in the following order Operat
76. be defined for any one PEDSYS record a maximum of 30 loci may be converted in any one run Dr 45 14 e TRANSLAT May 19 1999 TRIPLETS Program TRIPLETS extracts selected data from the separate records of Ego father and mother and places this information on a single record The file from which triplets are generated may be either a Master File or a pedigree file consisting minimally of records containing IDs for Ego and Ego s parents Triplets may be constructed for probands entered from either the keyboard or from a Proband Input File a file consisting of a list of either Sequential or Permanent IDs Introductory Display EDSYS program TRIPLETS Copyright 1992 1999 SFBR RIPLETS assembles data for Ego father and mother on the same record 1 Unlinked File EXAMPLE 3a LOCUS Sub directory Enter number file name or Q to quit gt 2 Case 1 Triplet data extracted from one or more Linked Files If files are linked data may be extracted from more than one file If this option is chosen the following display appears from which files containing the data may be selected Linked Files Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Data from more than one LINKED file may be selected for inclusion in an output record Enter numbers corresponding to file s above in the order that items are to b xtracted or RETURN to continue to next st
77. been selected the following display appears which permits further subgrouping of records separated by dashed lines within pages Define subgroups on page will be separated by dashed lines Y N gt This is followed by another Item List Display similar to the one from which page grouping key items were selected Note that the grouping feature requires that the file be sorted by one or more key items by which groups are defined Once items and groups have been selected the next instruction appears Enter number of copies to be printed 1 5 or S to select range of records to be printed gt It is not necessary to list all records in the file and printed output may be restricted to a specified range of records If S is chosen the following display is shown Enter range of records to be printed 1 32 gt 1 10 Enter number of copies to be printed 1 5 gt April 20 1999 LIST 26 3 Notes e LIST prints page and column headings at the top of each page The page heading includes the current date file title and listing page number The current date is taken from the computer s hardware clock and the file title is usually taken from the Code File Label Record However if files sort out or subset out are listed the file title is derived additionally from file SORTIN TMP or SUBIN TMP respectively see Temporary System Files Appendix A This makes it possible to include information a
78. below which shows the record found in file combine out default ungrouped format combine out Items 11 Top record 1 1 1 2 3 4 5 6 7 8 9 10 11 EGO DATE hgb DATE hgb DATE hgb DATE hgb DATE hgb Recl Recl Rec2 Rec2 Rec3 Rec3 Rec4 Rec4 Rec5 Rec5 DO15 1988 05 27 14 2 1989 03 24 13 5 1990 01 24 12 3 1991 01 08 13 2 1993 05 06 12 5 Enter lt n gt or lt n gt for new page lt n gt 1 1 to set top row gt or lt lt n gt to shift window I lt n gt 1 11 to set window L to lock columns N for new file F to find H for help Q to quit gt Note that entries corresponding to Items 2 and 3 from the original record appear in five sets with items in each set repeated from left to right in the order originally selected in Step 1 The source of each item on the new record designated by Rec1 Rec2 is placed in the first unused or the last mnemonic word of the output Code File combine cde Because the BROWSE display is limited to the first two mnemonic words this information sometimes cannot be seen If the item grouping option is selected items are grouped by type as shown below combine out i Top record 1 1 1 2 6 A 8 9 10 11 EGO DATE F F E DATE hgb hgb hgb hgb hgb Rec1 Rec2 Rec3 Rec4 Rec5 Rec1 Rec2 Rec3 Rec4 Rec5 D015 1988 05 27 1989 03 24 1990 01 24 1991 01 08 1993 05 06 14 2 13 5 12 3 13 2 12 5 Enter lt n gt or lt n gt f
79. birth registry data in which the identity of parents is known but parental birth records are not available and thus are not entered into the file If Ego s record contains one or more parental PIDs for which individual records are not present in the pedigree file answering y to the first query above instructs INDEX to create a record for each missing parent and assign a pointer appropriately to Ego s record Query 2 Create record for unknown parent when only one is known Y N gt A similar problem can occur when only one parent is known that is when one of the parental PIDs is blank Answering y to the second query above instructs INDEX to a create a record for the unknown parent and b place a PID for that parent in the appropriate place in Ego s record Normally Permanent Identification Numbers are kept as Data Type C in which case PIDs of newly created individuals start with the character followed by a sequential number equal to one greater than the number of previously created records If PIDs are kept as Data Type I not recommended newly created integer PIDs are incremented in the range lt i gt through lt n gt where lt i gt is one greater than the largest integer representing a PID in the file In some cases fields width of newly created PIDs may exceed the original width specified in the input Code File When this occurs INDEX halts execution with an instruction to increase PID field widths appropriately Note
80. by finding that entry in the field having greatest number of non blank characters determining the number of leading or trailing blanks in this field and then truncating the field by this number of characters on all records This process reduces field width as much as possible but prevents loss of non blank data 35 2 e REFORMAT April 19 1999 Subdivide an item Entry of 3 produces the following display Subdivide Birth Date YYYYM Segment 1 gt 4 lt Enter number of characters 1 8 to be assigned to this segment In this example the components Birth Date will be subdivided into three separate items corres ponding to YYYY MM and DD A Status Line appears at the top showing the label of the item to be subdivided Below this is an Item Ruler in which the colon symbol designates a character that has not yet been assigned to a subdivision or segment As a visual aid every fifth unassigned character is marked with a stroke 1 The number of the segment to be created appears next followed by a command line into which format information is entered In this example we create the first segment by assigning four integer characters and the mnemonic YEAR as follows Subdivide Birth Date YYYYM Segment 1 gt 4 lt Enter number of characters 1 8 to be assigned to this segment gt i lt Enter the Data Type of the segment C I D or R gt YEAR lt Enter a single mnemonic for this segm
81. by importing computer readable data assumes that data are available in the form of a foreign that is non PEDSYS ASCII text file containing one or more records for any individual in the Master File The Permanent ID of the individual must be included in each record It is important that this PID have exactly the same format as the PID in Master File records Other content and format requirements of these records are the same as those listed above for keyboard data entry Step 1 Procedures for creating a Linked Data from a foreign data file will vary depending on the record format of the foreign data file Character delimited format For records character delimited format follow the procedure outlined above for creation of a Master File using program TRANSLAT Fixed format The easiest way to create a PEDSYS Data File from a foreign data file with fixed format records is to run program ITEMIZE without selecting the Master File options If no input Code File is used you will be prompted for the field width data type and first mnemonic of each item In the case of a Linked Data File make sure that the Standard Mnemonic EGO or ID is used to identify the Permanent ID that must appear on each record If a Code File describing the structure of the foreign file is available it may used as input to ITEMIZE In this case also make sure that the Standard Mnemonic EGO or ID was used to identify 10 December 1996 Creating a Pedigree Databa
82. by which individuals are arranged in a sibship Reordering of sibships requires that parents of sibs be identified correctly and that parental sex is assigned properly A change in BIRTH date is not permitted if a EGO s parent as listed in the Master File does not list EGO as an offspring or b the type of this parent i e SIRE or DAM listed for EGO is not the same type as listed for its other offspring in the Master File If these conditions are found by cross checking PIDs of family members in the Master File the following errors may be reported lt ego gt BIRTH not changed EGO not found as offspring of lt sire gt in MF 71 lt ego gt BIRTH not changed EGO not found as offspring of lt dam gt in MF 72 lt ego gt BIRTH not changed DAM lt dam gt listed as SIRE of KID1 lt kidl gt in n 73 lt ego gt BIRTH not changed SIRE lt sire gt listed as DAM of KID1 lt kidl gt in MF 74 where lt sire gt and lt dam gt are PIDs of EGO s parents and lt kid1 gt is the PID of the first offspring of the parent all as given in the Master File These errors occur only when making changes to a record previously entered in the Master File Probable causes are a incorrect assignment of parental PID to EGO or lt kid1 gt in the Master File or b incorrect assignment of parental PID to lt kid1 gt in the Master File To correct these errors If a first re enter correct parent
83. case the marker is in genotypic form Here are some examples of mnemonic word sets for genetic markers Interpretation phenotype phenotype genotype genotype genotype 5 The Master Pointer File As explained above Sequential ID numbers in PEDSYS Master File records serve as pointers to the records of family members in the file Although these numbers make processing of pedigrees very efficient they are difficult to remember and it is usually more convenient to identify individuals in a data set by their Permanent IDs The Master Pointer File contains a record for each individual in the Master File The two items of this record are Ego s Permanent and Sequential IDs separated by a single June 12 1999 APPENDIX A e A 9 blank character used as a visual separator The FORTRAN format for the record is A lt f gt 1X 15 where lt f gt is the length of the Permanent ID as specified in the Code File The Master Pointer file is sorted by Permanent ID resulting in an ordered list or index that can be searched quickly to find any Permanent ID and its corresponding Sequential ID number The Sequential ID points to the location of Ego s Master File record from which pointers to other relatives can be used to assemble Ego s extended pedigree Master Pointer Files are automatically produced by the PEDSYS programs INDEX and SETMASTR but also may be created from a Master File by the appropriate use of SORT and REFORMAT Mas
84. cause the program to suppress production of output data files and to terminate with a FATAL ERROR message c INDEX checks human populations indicated by parental mnemonics FA and MO for nuclear family consanguinity father daughter mother son full and half sib matings Occurrence of such matings results in a warning in index err This check is done only when pointers to offspring and sibs are generated initial Choice 1 and Choice 2 shown in the Introductory Display Original input files remain unchanged making it possible to return to earlier versions of the data Output Choices 1 or 2 Master File produced If the input pedigree file is not already in Master File format individuals selected will be indexed and the first eleven items of a Master File record will be created If the input pedigree file is in Master File format individuals selected will be re indexed and the first eleven items of the Master File plus PEDNO and GEN will be replaced The newly generated index item for the additional individual selected in Choice 2 will immediately follow that individual s Permanent ID in the output record All other items will be placed in the same order as they appeared in the input record Choice 3 Master File not produced Newly generated indices for ID EGO SIRE FA and DAM MO will appear as the first three items in the output record Additional items will be placed in the order they are selected Choice 4 single individual
85. chosen appear together in this display Here Items 1 21 are from the Example Master File and are followed immediately by Items 22 26 from the Markers Quant P types File Step 3 Selecting Symbol Types and Attributes After text fields have been specified the following screen appears from which palettes containing codes specifying graphic symbols may be chosen In addition to PIDs of EGO father and mother Pedigree Draw needs only SEX coding to determine basic symbol representation a square or circle designating males or females respectively so that this next step may be skipped if no additional attributes are to be assigned to individual symbols in the pedigree 34 2 PREPDRAW May 4 1999 Pedigree Draw Palettes Standard pre defined symbol types Filled quadrants representing combinations of up to 4 traits Two character alphabetic codes Miscellaneous pre defined attributes shading etc r number corresponding to palette from which symbol types and attributes will be selected for inclusion on output records Enter C to continue to next step gt 1 Each palette contains 16 symbols or patterns that can be combined in various ways to signify characteristics of EGO as represented graphically in a pedigree diagram Entry of 1 here results in display of data items plus a list of standard symbol types found in Pedigree Draw Palette 1 Entries from this list are what appear in the legend box of Pedi
86. contains records for all ancestors identified by the program anc lt n gt out contains records for individuals making up a pedigree connecting a single ances tor to its proband descendants where lt n gt is the ancestor Sequential ID ANCESTOR 6 7 ancesall out contains records for individuals making up one or more pedigrees connecting all ancestors to their proband descendants ancestor err contains proband IDs entered from an input file that are not found in the input pedigree file 6 8 e ANCESTOR April 20 1999 APPEND Program APPEND joins two files whose records share the same format Introductory Display EDSYS program APPEND Copyright 1992 1999 SFBR APPEND joins two or more files whose records share the same format Code Files are compared for length and format type of each item If discrepancies are found error messages are displayed and joining of files is not per mitted Unlisted file EXAI PLE Enter number of the file or directory to use or Q to quit gt A second standard File List is displayed next from which the second of the two files to be joined is selected Standard Item List Displays are not used After two files have been selected and joined the following display appears lt filenamel gt lt ext gt lt fliename2 gt lt ext gt have been joined and written to file append out Enter A to append an additional file X to ex
87. contains records of individuals identified by PIDs all or some of which begin with the letter S followed directly by a number S10 S11 S12 etc In this case there is no way to distinguish between entry of the PID S10 and the Sequential ID Number 10 which must be specified in the command line with a leading S that is also as S10 The same problem may occur if PIDs begin with command characters I or i and Porp To circumvent this possibility the following alternates may be used lt n gt may be substituted for S lt n gt or s lt n gt lt n gt i Ikn gt or i lt n gt In the example just given specification of Sequential ID 10 would be 10 to distinguish it from PID S10 Likewise 5 may be substituted for i5 to specify that Item 5 be placed in the left most unlocked column The default characters were chosen to speed up command sequence entry by avoiding the use of the keyboard shift key The alternates are available in all relevant PEDSYS programs e To save screen space for data a maximum of two mnemonics per item are displayed in the header e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example browse subset out e The display on the next page illustrates output from program BROWSE using expanded screen dis play settings 130 columns by 52 rows which permit single page display of 19 items for all 32 records of the Example Master File
88. countped err In a large family it may be easier to locate the incorrect data entry by running the input data through program INDEX which in addition to a check for multiple PIDs identifies individuals whose birth dates are inconsistent with those of their parents COUNTPED finds all independent pedigrees by tracing connections between individuals using a FORTRAN adaptation of algorithms taken from program PEDSPLIT part of the LINKAGE pack age version 3 5 by M Lathrop and J M Lalouel COUNTPED s convention of counting generations down from the top of the pedigree can lead to ap parent anomalies because parents and offspring may not be assigned to adjacent generations For example in the pedigree below individual A is the father of Ego E If generations are assigned by counting up from Ego A would be assigned to Generation 2 left hand diagram Results of the COUNTPED convention are illustrated in the right hand diagram where it can be seen that generation numbers of Ego and A are separated by two Counting up from EGO Counting down from founders Pedigree Draw Frequently it is more convenient to group all unrelated individuals in the same pedigree such individuals are of course all assigned to Generation 0 If the input file contains a subset of a larger pedigree records for individuals appearing as parents on Ego s record may be missing In this case COUNTPED can either use or ignore information from Ego s parental IDs Par
89. displaying the icon view in the PedSys folder rebuild the DeskTop files on the hard drive volume by restarting the computer and pressing the Com mand Option keys together Click the OK button when asked if you want to rebuild the DeskTop file of the disk volume containing PEDSYS Fa 3 Running PedSys When the application PedSys is started a Launch window of named buttons is displayed with each active button representing an application stored in PedSys Progs This is the main point of reference for running applications and managing files An application may be initiated by clicking the appropriate button by typing the name of the application and pressing RETURN the first 3 4 letters of a name usually suffice or by using the up down arrow keys to highlight a button and pressing RETURN Functions such as Path In or Rename are triggered by clicking the button or by pressing the Command key plus the first letter following the Command key symbol in the button label Misc Example gt PedSys gt Misc Ex Out l General Data Management File Management Age AlterDat Browse howData DBFiler Translat Calc DelRecs Yerifier iil Append Reformat Code Report Tally Combine SetData Pedigree Management Genetic Management PedDraw D CKinship PrePDraw Arbor CountPed PrePDraw GenCheck Haplotyp PedTrim MakePed PedCheck GeneFreq FoundRep Triplets GenoMap PeelSeq Select a progra
90. ego gt is the PID of the record to be updated in lt filename gt UPD Error 21 may occur when adding new data to a Single entry Data File Error 22 occurs when making changes to data in either Single entry or Multiple entry Data Files Probable cause of Error 21 is double entry of data in a foreign file that is converted to PEDSYS format Probable cause of Error 22 is prior deletion of a data record which might occur if program DELRECS has been run before program SETDATA Changes and additions to Data Files are prohibited also if errors or conflicts are found in Permanent IDs PIDs of records in the Master File associated with the Data File containing records to be changed These errors are reported as follows lt ego gt Not found in Master File record not added to Data File 23 lt ego gt Not found in Master File entry not changed 24 where lt ego gt is the PID of the record to be updated in lt FILENAME gt UPD Error 23 may occur when adding data Error 24 when modifying data in either Single entry or Multiple entry Data Files Probable cause of either error is prior deletion of a Master File record between running ALTERDAT and SETDATA Fa Changes and additions to Multiple entry Data Files are prohibited if errors or conflicts are found in the internal pointers of records in the Data File containing records to be changed These errors are reported as follows lt ego gt Entry not changed no internal pointer in update
91. file that is by the data type codes listed in the input Code File but these defaults may be overridden by the data type of Conversion Table entries Numerical items types I R or D may be converted to character data in which case a warning is issued Entries for conversion of integer type I or real data type R in fields of the Conversion Table are automatically right justified Entries for character data type C are left justified although leading blanks are honored Data types of items referred to in the Conversion Table newitem tab are determined by data types of items the input file but values of test and change values must be defined unambiguously The table below gives examples of command sequences and their interpretations 29 6 NEWITEM April 19 1999 Data Type D I or R Interpretation 11 eq Is Item 11 equal to Item 8 whatever the numeric value 11 eq Is Item 11 equal to either Item 9 or Item 10 11 ne Is Item 11 equal to neither Item 9 nor Item 10 11 dt Is Item 11 less than numeric constant 8 18 eq Is Item 18 equal numeric constant 3 or 4 18 eq Is Item 18 entirely blank 18 eq Is Item 18 entirely blank 18 eq Does Item 18 contain a blank character in any field position IF IF IF EB IF IF IF DE VV VV VV VV Change Interpretation HEN gt 5 6 Set Item 5 equal to Item 6 whatever the numeric value EN gt 5 k6 Set Item 5 equal to numeric constant 6 EN gt 18 Dth Convert numeric item to
92. for Linked Data Files If Data Files are formally linked to Master Files see the description of Data Pointer Files and instructions for PEDSYS program DATALINK the associated Code File must be named lt FILENAME gt CDE where lt FILENAME gt is the name of the associated Data File For example SAMPLES CDE is the name of the Code File associated with the Example Data File SAMPLES XMP distributed with the PEDSYS package Code Files for Unlinked Data Files There are no fixed rules about naming unlinked Data Code Files but they conventionally take the form lt filename gt cde where lt filename gt is an arbitrarily chosen name that identifies both the population and the relevant data set It is a good idea to make sure that the first item on each record is a PID if there is any chance that they will be linked to a Master File in the future Code Files for Genetic Marker Data Files Data Files that contain genetic marker phenotypes and or genotypes require no special configura tion but if genetic data are to be displayed and analyzed correctly by programs GENCHECK GENEFREO and INFER some mnemonic words defining the phenotypes may have reserved forms as follows Mnemonic Word 1 This word consists of the name of the locus in full or in abbreviated form Examples ABO ADA APRT G6PD etc Mnemonic Words 2 4 The locus is assumed to be in phenotypic form unless any one of the the next three mnemonic words is GENO or G TYPE in which
93. gt In this program the usual asterisk that marks items chosen for inclusion is replaced by directional markers marks items to be sorted in ascending order marks items sorted in descending order EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING 15 Dam s Permanent ID SIRE S S 9 PATERNAL SIBSHIP SIZ Sex M F or U DAM S SE 10 MATERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exit Code EX ERNAL SIB SI 12 EGO Permanent ID 19 Mate s Permanent ID EX ERNAL SIB SI 13 Birth Date YYYYMMDD 20 PEDIGREE NUMBE EX L SIB SEQ 14 Sire s Permanent ID 21 GENERATION NU SORT Items to be sorted File MASTER XMP Enter numbers corresponding to items to be sorted in order of decreasing significance Precede item number with a D to sort in descending order Enter C to continue gt Items to be sorted in ascending order may be selected by entering item numbers alone or by preceding them with A for example a10 items to be sorted in descending order are preceded by a D example d13 Here selections have been made to sort the Example Master File in ascending order by Sex which results in Item 16 being marked by a and descending order by Generation Number which is indicated by the mark adjacent to Item 21 April 20 1999 SORT e 42 1 Confirmation Dis
94. gt F lt ALTERDAT LOG normally ON T gt T lt lst passwor gt pwd1 lt 2nd password gt lt 3rd password gt lt 4th password gt lt Li Zi 3 4 De 6 Tx 8 9 0 it Enter the number of the field to be modified Enter S to SAVE CONTINUE without saving changes gt Selection of choice 5 specifying the Locus Sub directory in the Edit File Group display above results in the following display EDIT Sub directory name gt LOCUS gt Note that only the name of the sub directory may be changed at this point To modify sub dir ectory files the sub directory itself must be selected in the introductory directory selection menu above A Command A Add a Descriptor Record to DBFILES makes the corresponding file accessible to PEDSYS programs but does not affect the file itself Entry of command A results in the following display ADD DBFILES entry M to add a Master File L to add a Linked Data File U to add an Unlinked File S to add a Sub directory R to return to initial function menu ADD Options M Addition of a Master File is normally done only in a new directory that a contains a new Master File and its associated Code File and Master Pointer File and b does not yet contain a copy of DBFILES Program DBFILER will create a new copy of DBFILES in this case Option M produces the following sequence May 27 1999 DBFILER 15 3 AD
95. has been specified Step 2 Specifying Text Fields Next items that will appear as text fields below the symbols representing individuals in the Pedigree Draw diagram are selected EGO SEQUENTIAL ID SIRE S SE DAM S SEQ FIRST OFFSPRING SEQ EXT PATERNAL SIB SE EXT MATERNAL SIB SE EXT FULL SIB SEQ UMBER OF OFFSPRING ERNAL SIBSHIP SIZ ATERNAL SIBSHIP SIZ ate s Permanent ID FULL SIBSHIP SIZE PEDIGREE NUMBER EGO Permanent ID GENERATION NUMBER Birth Date YYYYMMDD Ego ID Sire s Permanent ID ADA Phenotype Dam s Permanent ID APOB Pvu2a Genotype Sex M F or U Tot Ser Cholestero Exit Date YYYYMMDD APOAI Level Exit Code W 0 JU BWN FE JU amp N OH EPDRAW Select text fields Enter numbers corresponding to items to be included as optional text fields 5 items maximum Required items are pre selected All text items longer than 24 characters are truncated Enter C to continue gt PIDs of EGO FA and MO as well as SEX birth date and death date are pre selected here because they are automatically maintained as special purpose symbols and text fields in Pedigree Draw records Item 23 ADA Phenotype has been entered in the command line as the first of the five optional text fields in the example above Note that items from the Master File plus those from the Data File
96. have neither parents nor offspring 1 All to the same pedigr Pedigr 0 2 Each to a separate pedigr Enter number corresponding to choice gt 1 gt Beagles Enter population label for MAST gt This is a Dog Master File lt Enter file label for MASTER DOG Here a Master File Descriptor Record with extension DOG population label Beagles and file label This is a Dog Master File will be added to a newly created DBFILES Note that passwords have not been added this will have to be done with the edit feature of DBFILER If SETMASTER has been run previously the following display which controls the disposition of a previously created log file may appear setmastr log already exists Enter D to DELETE Log File A to APPEND to current Log File X to EXIT program Error Messages and Displays Program SETMASTR is usually run as the last step in permanently updating or creating Master Files Because its output plays such a critical part in the organization of pedigree databases consider able effort has gone into preventing errors from being incorporated into the data Protection from permanent damage is provided at three levels 39 2 e SETMASTR April 20 1999 Level 1 Errors that affect single records are recorded in the setmastr err file and the record in ques tion is not updated Level 2 Whenever possible the program is stopped before the final creation of new fil
97. in the output listing gt lt n gt or lt lt n gt where lt n gt is an item number as described above Entry of this sequence right or left justifies the character string in the field If the justification feature is used the usual asterisk marking items chosen for inclusion will be replaced by directional markers gt marks items to be right justified lt marks items to be left justified B A field of blanks may be entered with this command which produces a request for entry of field width item label and mnemonics Data type is automatically set at C K This command inserts a field containing a fixed string of characters The string must be surrounded by single or double quotes and its entry followed with entry of an item label and mnemonics Data Type is automatically set at C Output Width Adjustment Maximum printer width in characters is set in the DEVICES file If the width of the output record selected exceeds this maximum the following display appears The total width of the items chosen exceeds the record length of the file The limit is 133 characters The selected items when formatted add to 138 characters Please delete one or more items Press RETURN to continue gt Deletion of items is done with the standard record editing cycle see Appendix A SETTING DIREC TORIES and RUNNING PEDSYS PROGRAMS Requests for additional format information are displayed before the program is run
98. is created by program DBFILER see Chapter IV Creating a PEDSYS Database and Appendix A File Types Also listed in the Data Directory may be one or more Subdirectories Included here is the LOCUS subdirectory BO cde ADA ADA cde A POBpvu2a A POBpvu2a cde AllLoci AllLoci cde CA1 CA1 cde CandLoci CandLoci cde D1S1656 D1S1656 cde D1S3721 D1S3721 cde D1S515 D1S515 cde D2S1329 D2S1329 cde D2S326 D2S326 cde D3S1229 D3S1229 cde D4S1582 E 2 e INSTALLATION and SETUP Solaris 2 5 D4S1582 cde D5S1466 D5S1466 cde D6S1036 D6S1036 cde D7S23 D7S23 DBF IL cde ES DYS391 DYS391 cde ErrorDemo G6PD G6PD cde GGAT1A4 GGAT1A4 cde ErrorDemo cde June 10 1999 Note that names of Master Files Linked Data Files and System Management Files are in upper case to distinguish them from less permanent files that may be generated by PEDSYS programs We have found it best to limit files kept in PEDSYS Data Directories to those used as more or less stable input to PEDSYS programs and to keep them separate from working areas where output files accumu late This structure is enabled by the installation procedures given below d The PEDSYS Menu Directory The Menu Directory contains input data for the PEDSYS program menu seen when running program PEDSYS sa 2 Installation The Unix version of PEDSYS is provided on six compressed tar distribution files named PEDSYS lt
99. item and finally the new value to be added or substituted A NEW ENTRY record contains values of all items that are to be included in the record If the file is linked the first item will be the PID of the individual for which the record is to be added If the file is unlinked one of the items will have been designated as an identifier Records in lt filename gt DEL contain two IDs of records to be deleted The first is an ID as defined above and the second a recno representing the record s position in the file 4 14 e ALTERDAT April 20 1999 Files Input Output When CHANGING file contents Any Data File having an associated Code File and CODE STD If the Data File is linked a Master Pointer File and Data Pointer File are required When CREATING new files An appropriately named Code File and CODE STD are re quired If the Data File created is ultimately to be linked to a Master File a Master Pointer File is also required When CHANGING file contents Batch Mode lt FILENAME gt UPD and or lt FILENAME gt DEL Interactive Mode A modified input Data File and optionally ALTERDAT LOG When CREATING new files either Batch or Interactive Mode A Data File named lt FILENAME gt lt EXT gt whose Code File will have been created prior to data entry a April 20 1999 ALTERDAT e 4 15 4 16 e ALTERDAT April 20 1999 ALTMASTR Program ALTMASTR is a data entry and editing program for Master File records and is
100. items in the order they are to be joined into a single item Enter C to continue gt 21 Items selected are marked with asterisks in the usual way and the new composite item is added at the end of the record A label and a mnemonic set are created from a combination of the first mnemonics of the combined items A maximum of 10 items can be joined into one a maximum of 10 joined items may be produced B A field of blanks may be entered with this command which produces a request for entry of field width item label and mnemonics Data type is automatically set at C K This command inserts a field containing a fixed string of characters The string must be surrounded by single or double quotes and its entry followed with entry of an item label and mnemonics Data Type is automatically set at C R Entering this command produces a request for an integer seed 1 8 digits for a pseudo random number generator An item containing a randomly generated 10 digit fraction is added at the end of the record The seed is saved in the appropriate description field of the Code File reformat cde S Entering an s adds to each record an item containing an integer 1 99999 corresponding to the record s position in the file C Continues to confirmation step H Entry of an H produces the following help display pages 35 4 e REFORMAT REORDER items by entering the number corresponding to the item in the list in the order that items are to appear in t
101. let smallest data value determine lower bound gt 1 Enter EXCLUSIVE upper bound for value of NUMBER OF OFFSPRING Values equal to or greater than this bound will be tallied as a single class Enter RETURN alone to let highest data value determine upper bound gt 5 Enter number of classes or class width preceded by for NUMB OFFSPRING gt 4 If bounds on the tabulated value are not required response N to the first query above the program will begin processing tabulating the frequency of each distinct value of the item as a separate class In this example however choice Y was selected to set bounds on the tabulated variable NUMBER OF OFFSPRING which leads next to the options of setting its lower and upper bounds 1 and 5 respec tively Note that the lower bound is inclusive and the upper bound exclusive which means that in this example the range of offspring sibships tabulated is 1 through 4 Finally the choice is given to set the number of classes here 4 into which it is to be grouped An alternate means of grouping the tabulated variable is to specify class width In this example responding to the last query with 1 would yield the same result This sequence of options is repeated for each distribution to be tabulated Output Example Frequency Distribution Below is an display of file tally tab showing the frequency distribution specified for NUMBER
102. lt n gt pages from the current page The number of the top record on the page displayed in the upper right hand corner of the screen is updated Horizontal position remains unchanged The default value of lt n gt is 1 so that entry of RETURN alone advances the display by one page The total number of pages may be estimated by dividing the number of records by the number of records that appear on a single page see first Note below Page contents do not overlap that is the top record of the next adjacent page is set at one past the record displayed at the bottom of the previous page PID Entry of a valid PID linked files only sets the top of a new page at the corresponding record The new page is displayed with the horizontal window position unchanged S lt seq gt Entry of s followed by a Sequential ID sets the top of a new page at the corresponding record For Master Files and unlinked Data Files lt seq gt must be in the range 1 through lt nrecs gt where lt nrecs gt is the number of records in the file For Linked Data Files lt nrecs gt is the number of records in the Master File The new page is displayed with the horizontal position of the window unchanged lt n gt where lt n gt is an integer in the range 1 through lt nrecs gt the number of records in the file Entry of this sequence sets the top of a new page at the corresponding record The new page is displayed with the horizontal position of the window unchanged Note th
103. making it possible to add or remove Master Files linked and or unlinked Data Files from a database Enter RETURN to create a new DBFILES or Q to QUIT program gt has been created E to EDIT DBFILES entry ADD a new file or Sub directory to DBFILE DELETE a file or Sub directory from DBFILE edit NOTE VIEW DBFILES QUIT program on Commands E Command E Edit a Descriptor Record results in the following display EDIT File Group Example Master File Markers Quant P types Blood Sample Inventory Hemoglobin Levels LOCUS Sub directory r file number to be changed or R to return to initial function menu Here the Descriptor Record for the Markers Quant P types file has been selected for modifica tion The edit sequence is the same as that described in the ALTERDAT section Letters in parentheses in the display below and in subsequent displays refer to Notes a through s for the section describ ing the Directory File in Appendix A In this example a single password has been added Note The asterisk marking line 4 Field in data pointer file indicates that this variable may not be edited 15 2 DBFILER May 27 1999 EDIT QUANTGEN XMP File extension File name gt QUANTGEN lt Label gt Markers Quant Field in data pointer file gt 1 lt Multiple entry Data File T
104. mate pairs found on all records of file examped a 2 Each member of pair selected from a different source Choice 2 entered for pair formation specifies that all possible pairs will be formed by matching the first member selected from one source a file or list entered from the keyboard with the second member from a second source Each of the two sources must be chosen as follows April 20 1999 KINSHIP 25 5 Select the FIRST member of each pair from Keyboard Unlinked file subset out EXAI PLE Enter number above corresponding to the appropriate source of individuals gt 1 Select the SECOND member of each pair from Keyboard Unlinked file subset out EXAI PLE Enter number above corresponding to the appropriate source of individuals gt 3 Here the first member of each pair will be entered from the keyboard and the second from file subset out Next the type of ID by which pairs are to be identified is selected after which IDs of the first member of each pair is entered Enter RETURN if individuals are identified by Permanent IDs or S if by Sequential IDs gt Select FIRST member of each pair Enter Ego Permanent ID RETURN alone terminates entry gt ID071 lt ID gt ID067 lt ID gt ID045 lt ID gt lt ID Here the first member of each of three pairs has been selected The second member of each pair is
105. n gt 2 0 tar gz where lt n gt is an integer from 1 6 identifying each of the files These files are available on CD ROM ISO 9660 format and from our FTP site ftp www sfbr org pub pedmgt or the Southwest Foundation Web Page http www sfbr org Installation proceeds as follows note that write permission is assumed for the directory where PEDSYS is to be installed Step 1 Create a PEDSYS root directory pedsys and within this directory create sub directories bin menu and example Then within the example sub directory create the LOCUS subdirectory Step 2 Copy or download the compressed PEDSYS tar files to the location where the PEDSYS root is to reside Step 3 Uncompress each of the five file with the command gunzip PEDSYS lt n gt 2 0 tar Z Step 4 Extract the PEDSYS applications and data files from each of the the now uncompressed distri bution files with the command s tar xvf PEDSYS lt n gt 2 0 tar This will automatically place files in their appropriate directories and sub directories Step 5 Set the PEDSYS environment variable by adding the following line to the cshrc initialization file setenv PEDSYS pedsys_root where pedsys_root is the complete path name for the pedsys root directory assumes use of the Unix csh shell Step 6 Set the path to include the pedsys_root bin directory in the cshrc file June 10 1999 INSTALLATION and SETUP SOLARIS 2 5 e E 3 set path Spath pedsys
106. not added EGO already present 21 This error occurs only when adding a new individual to the Master File Probable causes are a incorrect choice of ADD mode in ALTMASTR b incorrect keyboard entry of EGO PID or c inadvertent double entry of the same individual To correct the error No action is required if c providing that all items in both entries are identical Otherwise re enter information for new individual using correct EGO PID use ALTMASTR in ALTER mode Re run SETMASTR using most recent Update and Master Files see note on renaming and deleting these files Group 3 Missing entry in Master File There must be a record in the Master File for every PID entered in the Update File that is EGO SIRE or DAM for which items are to be changed To assure this the Master File and records in UPDATE lt EXT gt that have already been processed are searched for the relevant PID The error is reported if the PID is not found in either list Errors reported may be lt ego gt lt mnel gt lt mne2 gt lt mne3 gt lt mne4 gt not changed EGO is not in MF 31 lt ego gt SIRE PID not changed lt newsire gt is not in MF 32 lt ego gt DAM PID not changed lt newdam gt is not in MF 33 where lt mnel gt etc are mnemonics identifying the item to be changed lt newsire gt is EGO s SIRE PID and lt newdam gt is EGO s DAM PID all as given in the UPDATE lt EXT gt record These er
107. overriding the default missing data criterion of exclusion 32 8 PEDTRIM July 8 1999 Records 11 13 specify the three values designated as unacceptable Although pedtrim tab may be used as input for subsequent runs of PEDTRIM it is best to rename this file after it is generated to avoid overwriting it Note e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example pedtrim subset out Files Input Any Master File or an unlinked pedigree file with an associated Code File The Standard Mnemonics File CODE STD Recursive use of output files is permitted that is file pedtrim out may be used as input to program PEDTRIM Output pedtrim out contains records of individuals remaining in the trimmed pedigree pedtrim cde defines the record structure of pedtrim out pedtrim tab contains the table of critical data items that determine the inclusion of indiv iduals in the trimmed pedigree se July 8 1999 PEDTRIM e 32 9 32 10 PEDTRIM July 8 1999 PEELSEQ Program PEELSEQ determines a peeling sequence Cannings et al 1978 from an indexed pedigree file Introductory Display EDSYS program PEELSEQ Copyright 1995 1999 SFBR EELSEO determines a peeling sequence from an indexed pedigr file Unlinked File Example Master File Enter number file name or O to quit gt Input f
108. plus or minus sign followed by the constant and a Y M or D Examples 17 2 5y 13 30d where 2 5 and 30 are constants Note days may be expressed as integers only The contents of a numerical item may be added to or subtracted from a date by beginning the command line with an asterisk Examples 17 23y 13 22d where 23 and 22 are the numbers of items containing numeri cal values Note days may be expressed as integers only Enter C to continue gt 14 4 DATES July 7 1999 Examples Here are examples of legitimate PEDSYS date formats accompanied by examples of their respec tive representations of January 1 2000 YYYYMMDD YYYMMDD 20000101 0000101 Note Two digit representation of year YY and YYMMDD is permitted as input to program DATES although it is not a legitimate PEDSYS date format and will result in an error message if encountered in input data to other PEDSYS programs DATES will not allow two digit representation of year in its output Three digit representation of year including YYY and YYYMMDD are permitted Calcula tions using three digit format assume that dates lie between A D 1200 and A D 2199 inclusive Here are some non PEDSYS calendar date formats recognized by program DATES accompanied by examples of their respective representations of January 1 2000 month dd yyyy DDMONYYYY LR January 01 2000 01Jan2000 000 003 dd mon yyy yyy mm dd yyyyJ 01 Jan 00
109. probands are identified by Permanent ID S if by Sequential ID gt p Here Permanent IDs have been selected Next limits must be set on the number of ascending generations starting from each proband from which common ancestors will be sought 27 2 e MAKEPED May 19 1999 Output File will include direct ancestors and both parents of direct descendants of each proband including probands mates Output File may contain more than one pedigree if multiple probands are selected Limits of genealogical depth set below apply independently to each proband selected Enter number of ASCENDING generations of probands kin to be included in pedigree 0 20 gt 1 Enter number of DESCENDING generations of probands kin to be included in pedigree 0 20 gt 1 Include probands FULL SIBS Y N gt n Include MATES Y N gt y Here sibs have been excluded with mates included in single ascending and descending generations from the probands have been selected Next proband IDs are entered Enter proband s Permanent ID RETURN alone terminates entry gt ID054 lt ID gt ID015 lt ID gt lt ID The diagram below shows probands ID054 and ID015 and their relatives included in the pedigree ID038 ID056 13 ID045 1 1D034 1D077 ID070 ID054 a d la r I o 0 20 21 ID071 1D049 Proband O Family members included within generational limits specified Pedigree Draw May
110. records for that ancestor all descendants among the set of probands chosen initially and all individuals that connect the ancestor and these des April 20 1999 ANCESTOR 6 5 cendants These files are automatically named anc lt seq gt out where lt seq gt is the Sequential ID of the ancestor selected Here Sequential ID 12 has been selected which specifies that the pedigree con necting this individual PID ID065 with two descendant probands will be constructed and saved in output file anc12 out If a is entered as many pedigrees as necessary will be constructed to connected all six individuals listed as ancestors with their respective descendants Entry of S saves the separate files containing pedigrees plus the table proband and ancestor files as described above The final output screen message for the example session shown here is as follows PRA KKK KKK KKK KK KKK KKK KKK KKK AAA AE AE AE KKK KK KKK KK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK ANCESTOR is finished Output is in directory h1 population bdyke example ancesall out hi ancl2 out ancesego out contains probands for whom pedigrees were constructed ta ancesanc out contains all ancestors identified by the program 5 ancestor tab contains table summarizing output ia Be sure to rename output files before rerunning this program KKK KKK KKK KK KK KKK KKK KKK KKK AAA AE AE KKK KKK KKK KKK KK
111. right most locked column Visibility of items in the unlocked portion depends on their number the width of the unlocked segment of the window and the position of the window as specified by the relevant command sequence The total formatted width of locked items may not exceed the width of the screen Notes Multiple records are shown a when a Permanent or Sequential ID Number is entered while a Multi ple entry file is being displayed or b when the command switches the display to a Multiple entry file Single records are shown when a Permanent ID Number a Sequential ID Number or the or commands are entered while a Single entry file is being displayed or if an individual has only one records in a Multiple entry file Currently there is no FIND function in SHOWDATA Output may not be directed to a file Alternates are provided for the leading command characters specifying Sequential ID and Item num bers This is because of the possibility of conflict between the defaults and PIDs that may begin with the same characters For example suppose a Data File contains records of individuals identi fied by PIDs all or some of which begin with the letter S followed directly by a number 510 S11 S12 etc In this case there is no way to distinguish between entry of the PID S10 and the Sequential ID Number 10 which must be specified in the command line with a leading S that is also as S10 The same problem may occur if PIDs beg
112. run to modify the Directory File by adding the name of the new Data File to the Unlinked Data File list si 10 December 1996 Creating a Pedigree Database 4 7 III PEDSYS PROGRAMS June 12 1999 PEDSYS PROGRAMS e 3 1 3 2 e PEDSYS PROGRAMS June 12 1999 AGE Program AGE calculates ages for all individuals in a file by finding the difference between two dates represented in Gregorian form order year month day One of these dates must be taken from the individual s record for example Master File BIRTH ENTRY or EXIT dates The other date also may be taken from the record or it may be entered as a constant from the keyboard either in numerical form or as the character string TODAY which takes the current date from the computer s hardware clock Introductory Display EDSYS program AGE Copyright 1992 1999 SFBR AGE calculates ages for all individuals in a file by finding the difference between two dates represented in Gregorian form order year month day 1 Unlinked File 2 reformat out 3 EXAMPLE 4 LOCUS Sub directory Enter number file name or Q to quit gt 3 After a file has been chosen the output format of ages to be calculated is selected Enter the number corresponding to the way in which age is to be output In years with fraction In months with fraction In days In years months and days EGO SEQ 9 PATERNAL SIBSHIP SIZ Exit Date YYYYMM
113. tab VERIFIER 47 1 47 2 VERIFIER June 5 1999 APPENDIX A Definitions Data and File Types June 12 1999 APPENDIX A e A 1 A 2 e APPENDIX A June 12 1999 A Definitions We have tried to avoid excessive use of jargon but there are a few useful terms that require defin ition Record A unit of data storage in which information is kept usually for a single individual PEDSYS records are a maximum of 1024 bytes characters long and contain only printable characters ASCII characters 32 126 except for the end of record mark EOR which consists of a carriage return ASCII character 13 in the case of the Apple Macintosh and Unix machines or carriage return and line feed ASCII characters 13 and 10 in the case of MS DOS and Windows File A collection of records In most cases all records in a PEDSYS file have the same length and format except for the last record which may consist of a single end of file mark EOF This is a CTRL Z ASCII character 26 It is useful to make a distinction between units of data storage records classes of information and values that data can take Consequently we define the following units Field A subunit of a record in which a single item of information is stored Up to 100 fields are permitted in a single record maximum field width is 99 characters Item A named class of information usually pertaining to an individual that is stored in a single field of a record Also
114. the first two characters are inter preted as alphabetic codes that serve as symbol attributes displayed in Pedigree Draw graphic output The Palette 3 default is shown graphically in the left hand panel of the figure below Code AZ signifies an unassigned attribute which can be edited in Pedigree Draw e Note Only one alphabetic code from Palette 3 may be assigned to a single individual May 4 1999 PREPDRAW 34 5 Negat e L E i i Palet Consultand Asterisk ive Postive Double Neg Neg Pos Pos Neg Double Pos te 3 Alphabetic Codes Be upper right es upper right Peirce up rt O 3 centered amp above Inserted T O Wide sym line Standard Palette 4 Misc Misc Bar above Gray fill Vert hatch Horiz hatch CD pisa hatch E E Custom cel Attributes Selection of Palette 4 shown graphically in the right hand panel in the figure above results in the followin OANA SW g display EGO SE SIRE S DAM S SI QUENTIAL ID EQ EQ FIRST OFFSPRING SI PATERNAL SIB EQ SE MATERNAL SIB FULL SIB SI ERNAL SIBS EQ ER OF OFFSPRING HIP SIZ SE JU amp ND H IATERNAL SIBSHIP SIZ ate s Permanen FULL SIBSHIP SIZE PEDIGREE NUMBE R EGO Permanent ID Birth Date YYYYMMDD Sire s Permanent ID Dam s Permane
115. the sum count mean and standard deviation of selected numerical variables on each record d measurements of selected items converted between conventional units and standard Syst m International D Unit s SI units and e Z scores computed on previously stored or computed numerical values Precision that is placement of the decimal point of numerical output can be controlled Introductory Display PEDSYS program CALC Copyright 1992 1999 SFBR CALC generates functions of one or more numerical variables Unlinked File EXAI PLE LOCUS Sub directory Enter number of the file or directory to use or Q to quit gt After a file has been selected from the Introductory File List the following display appears Functions of numerical values are performed in the order listed below Calculate ln log exp random no integer seq SI Units Find sum count mean Std Dev and Std Err of items on same record Calculate Z scores Set output precision place decimal point Quit without running program r number corresponding to function Functions are performed in the order listed above that is there is no provision for returning to sim ple calculations such as addition and subtraction etc after a sum mean and standard deviation of variables has been specified It is not necessary to perform all functions for example output precision may be set withou
116. this Code File or RETURN alone to save output as code tab gt Command Q Quit program without saving Code File Entry of this command makes it possible to quit program CODE without saving the Code File if it has been generated Confirmation is required before final exit n Option H Create a Code File for a Master File human population If a Master File is to be created from keyboard entry using program ALTMASTR entry of H automat ically creates and formats the first 11 Master File items SEQ FSEQ MSEQ KID1 PSIB MSIB FSIB NKID PSIBSZ MSIBSZ and FSIBSZ The next five Master File items EGO BIRTH FA MO and SEX appear on the screen with most entries filled in Exceptions which require keyboard entry are width and data type limited to C or I of the EGO PID field width of the BIRTH Date field and the data type of the SEX field which may be either C for M F U or I for 1 2 or 3 Widths of FA and MO PIDs are automatically set to the width chosen for EGO PID Subsequently starting with Item 17 the cycle of requests for information described below for Data File items begins making it possible to add optional items to the Master File record This constrained data entry is required to ensure that mne monics field widths and data types are correctly configured for processing with ALTMASTR Option N Create a Code File for a Master File nonhuman population Entry of N likewise creates and formats Master File
117. to a Master File Data Pointer Files are named DPOINT lt EXT gt where lt EXT gt is an extension identifying the population For example DPOINT XMP is the name of the Example Data Pointer File distributed with the PEDSYS package 7 Reusable Output Files Most PEDSYS programs direct their output to disk files An important distinction between output files and other Data or Code Files is that they are designated as reusable files that is files that are erased and rewritten each time a particular program is run This means that data from the previous run of the program is lost when the program is executed again unless the data has been copied into other files or the output files have been renamed However output files from one program may be used as input to a different program without copying or renaming and some programs permit recursive use of output files for example file inferl out may be used as input to program INFER PEDSYS programs produce several types of reusable output data files a Data Output Files Most PEDSYS output consists of records for individual population members These files share most of the characteristics of unlinked Single entry Data Files They are named lt progname gt out upper case on MS DOS machines where lt progname gt is the name of the program that produces the output and out is an extension that identifies the file as a Data Output File When a Data Output File is produced by any PEDSYS program
118. to the Master File to which the Data File is to be linked when prompted DATALINK produces an updated version of DPOINT lt EXT gt that contains the appropriate pointers between the Master File and Data Files DATALINK also generates a new version of lt FILENAME gt lt EXT gt with updated internal pointers if it is a Multiple entry Data File see note below Output file datalink err may reveal inconsistencies that require correcting the original data see notes for ALTERDAT in Chapter V A note on importing Multiple entry Data Files Recording multiple entries for the same individual may be handled in different ways depending on the foreign database software used If multiple entries for the same individual are already stored on separate records in the foreign file all that is required is to make sure that the records are formatted and sorted properly see the Multiple entry Data Files section in Appendix A for details prior to submitting them to program DATALINK to generate PEDSYS Multiple entry Data Files If on the other hand multiple entries for the same individual are stored on a single record it will be necessary to disassemble the sequence into separate identically formatted records using program REFORMAT Fa 46 Creating a Pedigree Database 10 December 1996 Creating an unlinked Data File from the Keyboard If a Data File is not to be linked to a Master File only two steps are required for its creation from the keyboard S
119. type I or real data type R should be avoided as many analysis programs treat trailing blanks after numbers as zeros e Blanks and constants may be inserted in any position in the record e Data Type of items whose field width is changed remains unchanged if leading blanks are added but are changed to C if trailing blanks are added Changes to dates result in a Data Type change from D to C Data Type of subdivided and joined items are changed to C e The R random fraction and S integer sequence features are identical to those in program CALC These functions may be used only once during the current run of the program e The random number generator used is a FORTRAN implementation of a hardware independent linear congruential algorithm described by R Sedgewick p 37 in Algorithms Addison Wesley Publishing Company Reading Massachusetts 1983 e Insertion of blank or constant items may be repeated during the current run of REFORMAT e New items created by the gt lt U L F J R and S commands cannot be re selected during the current run of REFORMAT e Warning Data loss may occur when reducing field width e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example reformat subset out April 19 1999 REFORMAT e 35 5 Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is
120. unique identifier for Ego Father and Mother Introductory Display COUNTPED 1 EDSYS program COUNTPED Copyright 1992 1999 SFBR corresponding to the pedigree to which they belong identifies genealogical links and assigns numbers to individuals 2 assigns pedigree size and generational position of each individual in the pedigree and 3 assigns a number designating the founder of each individual s paternal or maternal ancestral lineage Unlinked file EXAMPLE LOCUS Sub directory Enter number file nam gt 2 7 OL MO to quit After a file has been selected COUNTPED searches its Code File for the standard mnemonics as specified in CODE STD see File Types in Appendix A If standard mnemonics for both Sequential IDs and Permanent IDs are missing the following display appears from which IDs of Ego father and mother must be selected EGO SEQUE NTIAL ID SIRE S SE Q DAM S SEQ FIRST OFFSPRING SEQ EXT PA ERNAL 8 NUMBER OF OFFSPRING 9 PATERNAL SIBSHIP SIZE 10 MATERNAL SIBSHIP SIZE 11 FULL SIBSHIP SIZE SIB SE 12 EGO Permanent ID EXT MA ERNAL SIB SE EX SIB SEQ 13 Birth Date YYMMDD 14 Sire s Permanent ID Dam s Permanent ID Sex M F or U Exit Date YYMMDD Exit Code Pedigree ID Number Generation Number ate s Permanent ID
121. which the pedigr is generated must be an indexed pedigree file with an associated Master Pointer File Unlinked File Example Master File Enter number file name or Q to quit gt 2 I Define descendant population SUBSET first All living individuals Mating age individuals Individuals younger than mating age II Define founders All founders of living individuals All founders of mating age individuals All founders of individuals younger than mating age III Find risk of founder genome loss For each founder find 1 Number of descendants among living population 2 Number of descendants in mating age population 3 Number of descendants in younger than mating age population Proportions of total i e N i Sum N i IV Find potential for equalizing founder representation For each descendant class find Proportional founder representation a Order founders by risk of loss b For each founder order descendant by representation of this founder What to do with living founders Note Files Input Any Master File with an accompanying Code File Output foundrep out 19 2 FOUNDREP May 30 1999 GENEFREQ Program GENEFREQ calculates gene frequencies from phenotypic or genotypic data Introductory Display EDSYS program GENEFREQ Copyright 1994 1999 SFBR ENEFREQ calculates gene frequencies from genotypic or phenotypic data CA
122. will be modified so that the SEX code will be changed from U to b blank instead of 3 as originally specified When the ADD function is selected from the previous screen characteristics of the new item are specified as shown previously after which the table entry sequence display appears Entry of D results in the following instruction Enter number corresponding to entry to be deleted Exit from the program prior to data conversion is possible at this point Command S creates and or saves the Conversion Table in output file newitem tab command Q exits without execution Entry of C results in program execution a Using NEWITEM with an existing Conversion Table If option T has been chosen from the Introductory Display the following request appears on the screen Enter name of file containing conversion table gt When name of this file has been entered a Conversion Table display appears with edit delete save etc commands as described above 29 4 e NEWITEM April 19 1999 Notes e Shortcuts Two shortcuts may be used to speed entry of NEWITEM command sequences The first of these makes it possible to enter a full command sequence on a single line rather than in segments following the gt prompts at the bottom of the command entry screen For example entering the following sequence after the IF gt prompt IF gt 16 ne F and 16 ne U then 16 1 AND gt OR gt THEN gt ELSE gt
123. without adding pointers to offspring etc Any one individual Produces Master File Enter number above corresponding to choice H for HELP O to QUIT gt Once the indexing format has been selected a pedigree file is chosen from the following display Unlinked Pedigr Fil Example Master File Enter the number or name of the file to index gt 1 Each of the four choices for indexing format shown in the Introductory Display produces a slightly different result Choice 1 Index of EGO FA and MO producing Master File Choice 1 indexes EGO FA and MO adding Sequential IDs pointers of first offspring next oldest paternal maternal and full sibs number of offspring paternal maternal and full sibship sizes Pedigree Identification Number and Generation Number to produce a standard PEDSYS Master File When this option is selected a modified File List appears from which a pedigree file may be chosen No Item List is displayed INDEX searches the Code File of the pedigree file selected and if the required items are found see Notes below the following queries appear in sequence Query 1 Create record s for missing known parent s Y N gt April 19 1999 INDEX e 22 1 Many analysis programs require that the pedigree file contain a record for each PID that appears in the file Sometimes this requirement is not met when pedigrees imported from other databases have been assembled from
124. 0 000 01 01 2000001 Notes e Preferred PEDSYS date format YYYYMMDD conforms to International Standard ISO 8601 see Appendix A Data Types e Two digit representation of year is not allowed in PEDSYS except as input to program DATES Three digit representation of year assumes that dates lie between A D 1200 and A D 2199 e Integer values are preferably expressed with leading zeros to fill out full field width in output January 01 2000 000 01 01 etc However DATES will correctly interpret single digit represen tation of month or day so long as this digit is separated from other numbers by an alphabetic string or character 1Jan1999 1 1 2000 etc e Abbreviated month indicated by month code MON results in a three character representation i e 01 Jan 1999 Full alphabetic month specified by month code MONTH results in full spelling of the month name e In the case of simple date format conversion fractional representation of the partial year indicated by the F code is carried out to three decimal places Denominator of fraction is 365 days except for Leap Years when it is 366 days The fractional part of a year added to or subtracted from a date as a constant however is computed on the basis of a 365 day year that is Leap Years are not taken into account Likewise fractional months are based on a constant 30 day month If more precision than this is needed it is best to express an added age or time interval
125. 1 BROWS Ernur darai E E A vele E E AE E E AA 8 1 CALC e aA AE E O E 2 ae 9 1 CODE ire Rea 10 1 COMPINE LA ra a PALI 11 1 COUNTPER srl tri ARA e a AA 12 1 DATALINK A degni rire ANEETA EER e EE E RR ILLE 13 1 DATES Leida E Er Core 14 1 DBFILER dari nto AEA M E e ia a ire 15 1 DEERECS s T E AO E Aa AEA A AEEA ite E 16 1 DOWNCGODE iine pe ipa Rei a Reale st ee dre E E AA AE EEG 17 1 PN aia sr a of tA gad a RE E RS CV Re NN E A 18 1 FOUNDRER SR iii A ad Deal te en 19 0 GENEFREO inner re Aye andrea a ra 20 1 GENOMAPI nee anne Es Re ne Peer cama Pro Dies die REA 21 1 INDEX cechi ie 22 1 A ol AE Ge Nee eae E E A a ia N 23 1 ITEMIZE ne rio rere ne ALL Eli vai 24 1 KINSHIP cod encens die in oaa Sine ae R a ER a a a ia eaa HER 25 1 Lolli ea E EE E E EA EEE ee 26 1 MAREFED atene ia e i REN 27 1 MERGE lA DINI 28 1 NEWIFEM en ile Lea darei ei 29 1 NUCEA Mvi i III ne E E T ES O E E AA TBA OUTLIER ptt cua AD ii Bi I IO irta TBA PEDTRIM Ep AIDA INTRA UA 32 1 PEELSEQ mareen trae iia RIA raae gach a tetes 33 1 PREPDRA W cicatriziale 34 1 REFORMA ER Soe A o alii aE E ne 35 1 REFORE na AIRLINE 36 1 SEGCHECK selle plan PeR DER Pas lat RA rh 37 1 SETDA TA nets eletto dire LA tte SAUT ERSTE a LER EE 38 1 June 12 1999 iii SHOW bielle rate ai 40 1 SHOWDA TA Menace rer ne reine eee ee a Wer aa are ree Sa ai aae A EA ai A 41 1 SORT atri acd are et Wa gan Mea ee arabe dirai 42 1 SUBSE Pneu ride naa pasa Race Ra ie 43 1 TALLY Sica toi eta bed deine itat
126. 1 Jan 4713 BC true Julian base 3 arbitrary base date Examples YYYYMMDD yyy mm dd yyy f MONTH dd yyy ddmonyyy J1 etc Two digit year valid for input only Enter date FORMAT include separators if present RETURN to skip this operation or H for help gt A similar display but not permitting two digit year format appears after input date format has been entered from which output date format is selected When input and output formats have been chosen a confirmation step occurs Format of date representation for BIRTH Input YYYYMMDD Output YYYMONTHDD Is this correct Y N gt y 14 2 e DATES July 7 1999 Two digit representation of year is allowed only as input to program DATES but must be converted to three or four digit format in DATES output When this conversion is required the following dis play appears Two digit representation of year found in input Enter 1 to convert to a 20th Century date 1900 s 2 to convert years 00 through 09 to a 21st Century date 2000 s 3 to select alternate boundary dates between 20th and 21st Cent Choice 1 above assumes that all two digit dates occur prior to the year 2000 Choice 2 assumes that two digit dates from 00 through 09 represent years 2000 through 2009 while dates from 10 through 99 represent years 1910 through 1999 These arbitrary boundaries can be overridden with choice 3 which produces the following screen display
127. 15 d 19980118 B b 19961013 EDIT text and symbol selections EXIT program program without executing or saving table Enter letter abov corresponding to action to be taken Si Command C starts program execution S saves the Symbol Selection Table in file prepdrw2 tab and exits the program without further execution 4 b 19880831 1D066 B A2A2 b 19771029 B b 19820000 ID019 C A2A2 b 19870000 b 19880211 b 19960727 Pedigree Draw Q exits the program without saving the Symbol Selection Table Notes e Using PREPDRAW with an existing Symbol Selection Table If option T has been chosen from the Introductory Display a request for the name of the file containing a Symbol Selection Table appears When this file name is entered PREPDRAW compares May 4 1999 PREPDRAW 34 9 the mnemonic listings in the file with mnemonics found in the input Code File s A Symbol Selection Table Edit Display then appears If the input file s currently being read are not the same as those used during the original construction of the Symbol Selection Table entries in this display may differ from those of the original table a The current display contains only those text and symbol selection commands whose mnemonics match Code File entries which means that some of the original entries may be missing b PREPDRAW accepts the first occurrence of a matching mnemonic sequence which may res
128. 19720309 I to INSERT new Item D to DELETE numbered item T to change Data TYPE R to display an alternate R ECORD April 20 1999 The Item Ruler of the fourth item is now made up of symbols and labeled with the mnemonic SKIP The functional consequence of this is that the 32 characters in this field need not be included in records of the output file M Change MNEMONIC T Change Data TYPE Entering M lt n gt or T lt n gt where lt n gt is a number corresponding to a previously entered item produces a request for a new Mnemonic or Data Type respectively Changing the Mnemonic to SKIP or the Data Type to S designates the item chosen as a skip field I INSERT new Item D DELETE numbered Item Entry of I produces a request for the number of a previously entered item prior to which a new item is to be inserted Entry of D lt n gt where lt n gt is a number or range of numbers corresponding to a prev iously entered item or contiguous items results in deletion of those items Either of these operations results in a downstream frame shift that is all item boundaries to the right of the modified item are shifted right in the case of Insertion or left in the case of Deletion by the number of characters in the modified item Characters included in the unassigned portion of the record are shifted accordingly The width of an inserted item is limited to 1 through lt unchars gt where lt unchars gt
129. 1990 01 12 1992 05 08 1993 10 12 UU A Wa SU A A OP A O L H Vv POW DN BIRTH E EXIT DI 1974 05 05 1996 12 23 1 36 6 REPORT April 19 1999 SEGCHECK Program SEGCHECK tabulates offspring phenotypes or genotypes by parental mating type Single locus segregation tables may be constructed for offspring of a individual parents of one sex and their mates or b all parents of one sex and their mates Tabulation may be limited to parents of specific phenotypes SEGCHECK makes the initial assumption that the data are autosomal codominant phenotypes unless one of the last three mnemonic words associated with the Code File entry for a locus is GENO or G TYPE in which case the data are interpreted as genotypes See note below for procedures to follow if the phenotype selected is not a codominant autosomal Introductory Display EDSYS program SEGCHECK Copyright 1992 SFBR EGCHECK tabulates offspring phenotypes or genotypes by mating type NOTE All loci are assumed to b ither autosomal codominant phenotypes or genotypes Other modes of inheritance will yield invalid segregation tables 1 Unlinked File EXAMPLE 3 LOCUS Sub directory Enter number file name or Q to quit gt Because SEGCHECK must extract data from multiple family records the program requires the use of indexed IDs f
130. 3 647 R Floating point decimal numbers Blanks are treated as zeros in PEDSYS floating point computations except in programs CALC and TALLY where blanks may signify missing values Floating point numbers are also right justified PEDSYS floating point input from disk or keyboard is limited to ten digits excluding the decimal point 0000000001 through 9999999999 in June 12 1999 APPENDIX A e A 3 absolute value Output is formatted as F12 5 giving a range of 0 00001 through 999999 99999 in absolute value Internal computations are normally done in double precision floating point arithmetic giving an absolute range of 2 23E 308 through 1 79E308 with precision of one part in 10E16 on the IBM PC Dates Dates are kept in Gregorian numerical form with order year month day as specified by International Standard ISO 8601 The ISO 8601 standard primary notation is YYYY MM DD but the standard also specifies alternate formats including omission of hyphens YYYYMMDD the convention used in PEDSYS Like the ISO 8601 standard PEDSYS permits representation of year without month or day PEDSYS date formats differ from the ISO 8601 standard as follows e Although four digit representation of year YYYYMMDD and YYYY are preferred PEDSYS will accept and compute with the shortened three digit year forms YYYMMDD and YYY Cal culations using these formats assume that dates lie between A D 1200 and A D 2199 A leading zero in three digit represent
131. 5 89685 I I I als I I I ag T o o o oo oo 0O Gr Di O Di Enter lt n gt or lt n gt for new page lt n gt 1 27 to set top row gt or lt lt n gt to shift window I lt n gt 1 33 to set window L to lock columns N for new file F to find H for help Q to quit gt Here the computed values for individuals with more than 2 measurements remain unchanged from the previous display but that the pooled inter individual standard deviation 1 26833 has been substituted for the unadjusted values for ID077 ID113 and ID124 and that standard errors have been changed accordingly 3 Calculating Z scores Z scores transforming numerical values to a standard Normal distribution can be calculated by selec ting Choice 3 in the Introductory display and in the sequence of commands following the confirmation step of the primary functions of Choices 1 and 2 4 Setting output precision Precision of numerical variables sent to the output file calc out that is the number of digits to the right of the decimal place may be set by selecting Choice 4 in the Introductory display and in the sequence of commands following the confirmation step of the primary functions of Choices 1 2 and 3 However precision setting is selected the following display appears EGO SEQUENTIAL ID 9 PATERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD SIRE S SEQ 10 MATERNAL SIBSHIP SIZ 18 Exit Code DAM S SEQ 11 FULL SIBS
132. 65 2 00 4 ID042 3 00 Enter Ancestor SEQ ID from list above or press RETURN to continue gt 12 Here ancestor 12 PID ID065 has been selected producing the following display tor 12 PID ID065 is common to the following probands EQ PID 20 IDO71 21 ID049 22 ID069 Enter C to continue gt Entry of C or RETURN re displays the ancestral list display previously generated Command N Generate a list of ancestors for a new subset of probands This command produces a re display of the following screen from which ancestors of a new subset of probands may be chosen A list of individuals that are ancestral to at least lt n gt probands will be generated Enter lt n gt the minimum number of proband descendants that each ancestor must have in order to be included in the list 2 3 gt 2 Here ancestors common to any two or more of these individuals has been selected which then produces the following display 6 4 e ANCESTOR April 20 1999 6 ancestors have been found that are common to at least 2 probands Ancestor SEQ only proband and ancestor files connecting ancestors to their descendants gt p Command S Save only proband and ancestor files PID ID065 ID042 ID045 ID034 ID047 ID062 No Pro Av No bands Steps 00 00 00 00 00 00 Enter D to display a list of proband descendants of an ancestor above N to generate a list of ancestors
133. 999 Item No Length Item name Mnemonic Ego Sequential ID SEQ Father s SEQ FSEQ other s SEQ SEQ First Offspring SEQ KID1 Next Paternal Sib SI PSIB Next Maternal Sib SI SIB Next Full Sib SEQ FSIB Number of Offspring NKID Paternal Sibship Size PSIBSZ aternal Sibship Size SIBSZ Full Sibship Size FSIBSZ Ego Permanent ID EGO or Birth Date Yr Mo Da BIRTH or Father s Perm ID FA or other s Perm ID O or Sex M F U or 1 2 3 SEX Exit Date Yr Mo Da EXIT Exit Code EXCODE Pedigree ID Number PEDNO Generation Number GEN W CO CO O1 O1 O1 O1 O1 O1 wo 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 9 0 HHQUAQAQ QB QHH AHH HH HH HH HH 2 Code File may contain additional items position not fixed Eight digit dates preferred Optional e Choice 2 Master File records containing the index of an additional individual include all items shown in table above with new field of Sequential IDs appearing as an item immediately following the PID of the individual selected for indexing as well as additional items included in the input file e Choice 3 Minimally only Sequential IDs of EGO FA and MO are included on output records if no items are selected in this mode Additional items are included only if selected from input records e Choice 4 In this mode all items present on input records are included on output records with the new field o
134. A B A O O A A B HHHHHKH HHKHHHKHKH HKHHW D W Enter lt n gt or lt n gt for new page lt n gt 1 32 to set top row gt or lt lt n gt to shift window I lt n gt 1 4 to set window L to lock columns T to change instructions N for new file F to find H for help Q to quit gt In contrast file infer2 out consists of records containing Ego PIDs from the input locus file initial phenotype that is as it appears in the locus file the inferred phenotype the a priori genotype the inferred genotype and two mnemonics identifying the locus Phenotype fields are left blank if inferences are made from genotypic data The file contains a record for each individual for which an original type is available or for which a phenotype or genotype can be inferred An example of the contents of infer2 out again with the ABO locus as input is shown below infer2 out Top record 1 32 1 2 5 6 ID INITAL INFERD PHENO E F GENO D015 D019 D034 D038 D042 D045 D047 D049 D054 D055 D056 D061 D062 a a 0 ABO b b 0 ABO a a 0 ABO b b ABO a a 0 ABO b 0 ABO 0 0 0 0 ABO 0 0 0 0 ABO a a 0 ABO a a 0 ABO b b 0 ABO a b a b ABO a b ABO A Py ene ee OO OOOOCCOOOOC CO o Gi GG dI di I I I I I I al I I I al I I Enter lt n gt or lt n gt for new page
135. AAAKKAAAKKAAAKAAAAKAAAAKAAAKKAAAKAKAAAAAAAAKAAAAAKAAAKAKAAAAAAAAAAAAKAAAA and or kkkxkxkxkkxkxkxkkkxkxkxkkkxkxkkkkkxkxkkkkxkxkkkxkxkxkxkkkxkxkkkkxkxkxkxkkxkxkxkxkkkxkkxkxkkxkkxkxkkxkkkxkkkkkxkkkkxk To complete the process of changing MASTE it will be necessary to run program D R lt ext gt ELR ECS AAA HEHE KKK KK KKK KK KKK KKK KKK KKK KKK KKK KK KKK KKK KK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK 5 4 e ALTMASTR April 20 1999 Notes e Parental records must be entered prior to entry of offspring e ALTMASTR saves changes and additions in file UPDATE lt EXT gt which is used in turn as input to program SETMASTR Because deletion of records requires extensive adjustments of the pointers upon which the PEDSYS file structure depends a somewhat different procedure is followed Deletions are saved by ALTMASTR in file DELETE lt EXT gt which is used in turn as input to program DELRECS ALTMASTR creates files UPDATE lt EXT gt and or DELETE lt EXT gt but the program will not run if files with these names are present at start up This is because the existence of these files implies that SETMASTR or DELRECS the ensuing programs in the two step Master File update process have not been run successfully Normally SETMASTR and DELRECS eliminate files UPDATE lt EXT gt and DELETE lt EXT gt respectively by converting them to backup files UPDATE OLD and DELETE OLD after permanent changes have been m
136. AL SIBSHIP SIZE Sex M F or U DAM S SEQ 10 MATERNAL SIBSHIP SIZE Exit Date FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZE Exit Code ERNAL SIB SE 12 EGO Permanent ID Pedigree ID Number ERNAL SIB SE 13 Birth Date Generation Number SIB SEQ 14 Sire s Permanent ID ate s Permanent ID File MASTER XMP Enter numbers corresponding to dates to be converted Enter lt i gt lt n gt Y M D to add or subtract lt n gt years months or days from date lt i gt before conver sion Enter lt il gt lt i2 gt Y M D to add or subtract contents of item lt i2 gt from date lt il gt Enter C to continue H for help gt Commands Simple conversion of date format is initiated by entering a number corresponding to an item containing a date In order to preserve the freedom to input dates having many different formats program DATES makes no assumptions about the Data Type of the item to be converted which means that it is quite possible by mistake to select an item that does not contain a date This error may or may not be detected when the program checks to make sure that the input field width read from the Code File is consistent with the input date format selected as shown below In general however it is left to the user to know which fields in the input file contain calendar dates and what their format is Ju
137. AMPLI Items 9 Recs 3 s many complete items as will fit on the screen Columns LIFO Page 1 1 FilePos 1 96 6 7 8 9 E ANIMAL PROJ COMMNT PNTR E E TAKEN ID097 ID097 ID097 W219 219 R219 1988 12 22 TYG 1980 07 01 9MI 1980 07 01 2MI LOW CRIT L L HIS wu Enter or lt n gt for new page top row lock columns O to change order help Q to quit gt Commands PID window providing that there is a record or lt lt n gt to shift window STATUS STATUS HLM HL HL HOSP HOSP to set L to H for PID S lt n gt 1 32 I lt n gt 1 9 to switch files or lt n gt 1 96 to set window N for new file Entry of a valid PID displays at least one corresponding record at the top of the display for the individual in the file If the file is a Single entry file only one record is shown if it is a Multiple entry file multiple records of the individual chosen will be seen The screen displayed ventory File S lt n gt where lt n gt is a Sequential ID Numb Sequential ID displays at least one cor below results from entering PID ID042 in the Sample In er of an individual in the Master File Entry of a valid responding record at the top of the display window providing that there is a record for the individual in the file If the file is a Single entry file only one record is shown if it is a Multiple en try file multiple rec
138. AW See Appendix B Program TRANSLAT Format Translations for more information on Pedigree Draw 4 4 formats z 45 4 e TRANSLAT May 19 1999 ONE WAY CONVERSIONS PEDSYS files may require some preparation before they can be converted to a form that can be used as input to genetic analysis programs CRI MAP Green et al 1990 FISHER and MENDEL Lange et al 1988 LINKAGE Lathrop and Lalouel 1984 PAP Hasstedt 1989 S A G E Elston et al 1986 and SOLAR Almasy and Blangero 1998 These requirements are a Records from only one PEDSYS file may be used as input which means that vital statistics and genealogical information must be combined with marker and quantitative data on the same record using program MERGE etc b Data required are IDs for Ego and Ego s parents Ego s sex pedigree ID as well as phenotypes and genotypes c Marker data must be in genotypic form However TRANSLAT will convert autosomal codominant phenotypes to genotypes if phenotype symbols conform to PEDSYS naming conventions see Appen dix C Rules for Genotype and Phenotype Nomenclature or if the loci are listed in a Genotype Phenotype Map File see Appendix A Definitions Data and File Types After a file has been selected TRANSLAT searches its Code File for the mnemonic SEX If not found the program terminates with an error message TRANSLAT makes the default assumption that an item with the mnemonic PEDNO produced by programs INDEX and CO
139. Code EX ERNAL SIB SI 12 EGO Permanent ID 19 Mate s Permanent ID EX ERNAL SIB SI 13 Birth Date YYYYMMDD 20 PEDIGREE NUMBE EX L SIB SEO 14 Sire s Permanent ID 21 GENERATION NU COMBINI Pick items to be grouped File MASTER XMP Enter numbers corresponding to items to be included in the combined record Enter A to include all items C to continue to next step gt April 19 1999 COMBINE 11 5 Here we have chosen Ego s Permanent ID and Birth Date Items 12 and 13 for inclusion on output records The results of combining these items can be seen in the display from BROWSE below which shows the records found in file combine out Items have not been grouped so that PIDs alternate with birth dates for as many offspring as there are in each full sibship combine out 1 2 SIRE DAM 3 ID Recl 4 BIRTH Recl Items 8 1 14 6 BIRTH Rec2 Top record 8 BIRTH Rec3 5 ID Rec2 7 ID Rec3 D015 D038 D045 D054 D055 D056 D061 D062 D063 D080 D095 D109 D109 D124 D019 D042 D034 D068 D065 D066 D042 D047 D065 D083 D097 D103 D111 D113 D067 D063 D071 D069 D034 D047 D065 D015 D054 D103 D109 D113 D124 D130 1996 07 27 1980 11 28 1993 03 18 1996 10 13 1987 06 23 1982 00 00 1981 07 05 1987 00 00 1986 12 15 1987 06 26 1985 08 14
140. D ID015 ADA Phenotype APOB Pvu2a Genotype Tot Ser Cholesterol 140 122 APOAI Level 144 0 179 0 Enter F to find next occurrence of Tot Ser Cholesterol Press RETURN to end search Enter W to write record gt Alternatively the Item List display can be bypassed by entering F an item number a relational and the value sought all separated by blanks which leads directly to the request for a starting record number For example entry of f 4 eq 140 at the command line is equivalent to the sequence described above Subsequent records found where the item sought has the same value by entering F again etc The message End of search appears when the value sought is not found in subsequent records in the file The message will also appear if the value is not found at all in the file A substring feature permits a search for a sequence of characters that occurs at any position in the field occupied by the item For example the substring 1966 would search for all occurrences of the year regardless of the month or day included in the date field Notes e Permanent IDs can be used to select individual records only from Master Files and their Linked Data Files This is because a Master Pointer File containing indexed PIDs is required for the binary search algorithm used to locate individuals by these IDs Records in Unlinked Data Files and files chosen with the unlinked file option in the File List Display
141. D Mas gt DOG lt Enter a 3 character file extension identifying the new Master Fil gt Beagles Enter population identifier for the new Master Fil MASTER DOG may be protected with up to 4 passwords gt pwdl lt Enter lst password gt pwd2 lt Enter 2nd password gt lt Enter 3rd password gt Beagle Master Fil lt Enter label for MAST Here a Master File Descriptor Record with extension DOG population label Beagles two pass words and file label Beagle Master File has been added to a newly created DBFILES L Option L causes a Descriptor Record for a Linked Data File to be added to a previously created DBFILES that already contains a Master File Descriptor Record ADD Linked Data File 1 MASTER XMP Enter the number corresponding to the Master File to which the Data File will be linked gt 1 When the new file name and a Master File have been selected the following display appears DD Linked Data File EWDATA lt Enter Data File name without extension Is this a Multiple entry Data File Y N gt n LOG normally ON for this file Y N gt y NEWDATA XMP may be protected with up to 4 passwords gt pwdl lt Enter lst password gt lt Enter 2nd password gt New Data File lt Enter label for NEWDATA XMP 15 4 DBFILER May 27 1999 Here a linked Single entry Data File named NEWDATA XMP ha
142. D Tot Ser Cholesterol 13 DAM S SEQ x Sex M F or U APOAI Level x PEDIGREE NUMBER Discrete Trait RANSTEST XMP TRANSLAT Select data Enter numbers corresponding to QUANTITATIVE data items to be included in output Required items have been pre selected Enter C to continue to next step gt 8 9 Items 4 and 5 and 11 13 Sequential IDs have been chosen are preselected and are protected from further change Items 8 and 9 represent quantitative data variables that may be selected for inclusion in May 19 1999 TRANSLAT 45 7 the output file Two additional blank variables Variance Covariate and Conditioning Status are automatically added to the record if they are not listed in the Item Selection Display as input options Notes on S A G E output e In addition to the conventional PEDSYS output file translat out and translat cde S A G E REGC translation produces two additional small files named fsp par and sageregc fmt respectively See Appendix B Program TRANSLAT Format Translations for more information about S A G E REGC formats e If variables Variance Covariate and Conditioning Status are included on records in the input file for translation to S A G E REGC they must be given single mnemonic words VARCON and CNDSTT respectively These mnemonics are assigned automatically in the output Code File translat cde if the variables are not present on in
143. DD SIRE S S 10 MATERNAL SIBSHIP SIZ Exit Code DAM S SE 11 FULL SIBSHIP SIZI ate s Permanent ID FIRST OFFSPRING SEQ 12 EGO Permanent ID PEDIGREE NUMBER NEXT PATERNAL SIB SI 13 Birth Date YYYYMMDD GENERATION NU NEXT MATERNAL SIB SI 14 Sire s Permanent ID EXIT BIRTH NEXT FULL SIB SEQ 15 Dam s Permanent ID NUMBER OF OFFSPRING 16 Sex M F or U 1 2 3 4 5 6 7 8 AGI Select dates File MASTER XMP To find the difference between two dates enter the first date a minus sign or blank and the second date Values may be specified as a number corresponding to a date in the list above a number preceded by a D or the word TODAY examples 17 13 D19590631 13 TODAY 17 Enter C to continue to next step gt lt COMMAND June 12 1999 AGE 3 3 Here age based on the difference between Birth Date and Exit Date in the Example Master File has been selected and the resulting new value appended as Item 22 Notes e Preferred PEDSYS date format YYYYMMDD conforms to International Standard ISO 8601 see Appendix A Data Types e All dates used in a calculation must have the same format YYYYMMDD YYYMMDD YYYY or YYY where Y year M month and D day These formats are specified by the length para meter in the Code File as 8 7 4 or 3 respectively A leading zero in
144. DD Sire s Permanent ID and value EQ or NE 1 32 Dam s Permanent ID M F or U YYYYMMDD Sex Date t Code ate s Permanent ID PEDIGREE NUMBER GENERATION NU Exit Exi ER Enclose substrings in or RETURN to start at In this example the Master File will be searched for the first record in which the number of off spring Item 8 has the value 2 When a record containing the item sought is found it is displayed on the top line of the display page in the format of the version selected when the program was started MAST 12 ID DO4 D06 DOS D06 D04 D01 D06 D04 D06 D03 H H ee H R HA H H H H Enter Press gt ER XM dl a4 SE 2 6 5 2 5 9 3 9 10 7 11 5 12 4 13 p 0O PN O BoP hb N 4 Not iS ct o sasa SW ro RETURN to end search April 19 1999 to find next occurrence of NUMB Items 21 5 6 7 8 Top record 4 32 9 10 11 PSIB MSIB FSIB NKID PSIBSZ MSIBSZ FSIBSZ 12 0 10 17 o o ooo oo o ooo o o oo o o ooo o D amp NW rNNFrFr_N ER OF OFFSPRING E H t LR O OO 5 N LP DP O OO HRK BROWSE 8 5 Alternatively the Item List display can be bypassed by entering F an item number a relational and the value sought all separated by blanks which leads direc
145. DELRECS must be run if records are deleted More than one file may be changed or created per run Batch Mod changes entered at the keyboard are stored in one or more temporary Update Files used in turn as input to SETDATA and or DELRECS Only one file may be changed per run an appropriate Data Code File must accompany the Data File used by his program Enter C to CHANGE a file Interactively N to start a NEW data file Interactively B to enter BATCH updates for a single file Q to QUIT program ALTERDAT has two modes of operation In Interactive Mode options C and N above permanent changes except for deletions of records are made directly to Data File records in a single step In Batch Mode option B the program becomes the first step of a process by which a temporary Update File is created and used in turn as input to program SETDATA which incorporates changes permanently into the Data File selected When either mode is selected a Standard File List Display sequence appears Interactive Mode Unlinked File EXAMPLE Enter number of file or file group to be altered or filename gt 2 Specify the Linked Data file to be updated 1 Markers Quant P types 2 Blood Sample Inventory Enter a file number gt 1 April 20 1999 ALTERDAT e 4 1 LINKED DATA FILES Linked Single entry Data Files A linked Single entry Data File Markers Quant
146. Data Files in the Data File Count Record is displayed while in Edit Mode the field is set automatically by DBFILER and cannot be changed manually sa Files Input A non empty DBFILES is required in REMOVE or EDIT mode A Master File is required when adding a Data File A Data Pointer File DPOINT lt EXT gt is required when adding or removing any Linked Data File other than the first Output DBFILES is the newly created Directory File DBFILES OLD is a backup copy of the Directory File prior to running the program DPOINT lt EXT gt is created when the first Linked Data File is added DPOINT lt EXT gt is modified and rewritten when a Linked Data File is added or deleted T May 27 1999 DBFILER 15 9 15 10 DBFILER May 27 1999 DELRECS DELRECS is a second program of the two step process required to make changes in both Master Files and Data Files linked or unlinked The program uses information from special purpose output files named DELETE lt EXT gt produced by program ALTMASTR in the case of Master Files and lt filename gt DEL produced by program ALTERDAT in the case of Data Files Introductory Displays EDSYS program DELRECS Copyright 1992 1999 SFBR DELRECS updates a Master File from changes stored in DELETE lt EXT gt Master File and linked Data File records are deleted and MPOINT lt EXT gt and D s POINT lt EXT gt are regenerated Files as they were b
147. Donor file 5 APOAI Level Ego ID ADA Phenotype 3 APOB Pvu2a Genotype 4 Tot Ser Cholestero DONOR File QUANTGEN XMP Items from DONOR file ERGE Enter numbers corresponding to items shown above in th be appended to merged record Enter A to list all items to next step gt order they are to C to continue After Standard Confirmation two requests for additional information are displayed in sequence before the program is run that have no Y N Include records from MASTER XI corresponding entry in QUANTG gt Y TARGET file DONOR file D In addition to saving merged records in file merge out Save records from MAST ER XMP ET file no corresponding entry that have in QUAN XMP DONOR file These records will be placed in file nomergel out Save records from QUANTGEN XMP OR file that have no corresponding entry in MASTER XMP TARGET file These records will be placed in file nomerge2 out Save unmatched records as described in both 1 and 2 above Enter number abov or press RETURN to continue to next step gt corresponding to choice The first query controls the content of output file merge out The second makes it possible to save records from either the Target or the Donor files that cannot be merged that is records that do not shar
148. E lt EXT gt and DELETE lt EXT gt that are used in turn as input to programs SETMASTR and DELRECS respectively The ALTMASTR SETMASTR DELRECS program sequence is used to make changes in Master Files The S A G E REGC option of program TRANSLAT produces files named fsp par and sageregc fmt each of which contains a single FORTRAN format statement used as input to S A G E REGC Names of these special purpose output files are displayed on the screen when processing is done Associated Code Files are not produced June 12 1999 APPENDIX A A 11 Note See also Section 14 Temporary System Files starting on page xxxx below 8 Backup Files Several of the File Management Programs produce output files that are updated or edited versions of pre existing Data or Master Files These programs automatically replace the old files with new versions but for safety s sake they also save the old file with the extension OLD For example new population members might be added to the Example Master File MASTER XMP with the programs ALTMASTR and SETMASTR ALTMASTR produces UPDATE XMP which is used in turn as input to SETMASTR SETMASTR generates an updated version of MASTER XMP and also saves the file as it was before new population members were added under the name MASTER OLD Likewise UPDATE XMP is automatically renamed UPDATE OLD 9 The Directory File A PEDSYS Master File and its associated Data Files are normally contained in an independent
149. File Creation of a Multiple entry Data File that will be linked to a Master File proceeds in much the same way as with the Single entry case described above Two differences are that more than one record per individual is permitted in the file and an Internal Pointer with value 0 is automatically append ed to each record created ALTERDAT output file lt filename gt lt ext gt must then be used as input to program DATALINK to complete the linking process April 20 1999 ALTERDAT e 4 11 da UNLINKED DATA FILES When the Unlinked category has been selected from the Initial File List a list of unlinked data files is displayed A file is then selected from this list or alternately a file name is supplied and the file is identified as a Single or Multiple entry Data File Unlinked Single entry Data Files Linked Data Files require that EGO PID be the first item on the record This is not a requirement for unlinked files which need not contain family data However ALTERDAT requires that at least one item on each record contain an identifier whether or not it is a PID The width of the item selected as an identifier must be no greater than 9 characters however EGO Permanent ID 3 Sire s Permanent ID 5 Dam s Permanent ID Tot Ser Cholesterol 4 Tot Ser Cholesterol 6 Tot Ser Cholesterol ERDAT Identification field File merge out Enter the number corresponding to the item above that uniquely identifies each record
150. File is saved as a backup under the name lt FILENAME gt OLD datalink err contains information about Data Records for which no corresponding record can be found in the Master File Fa April 20 1999 DATALINK 13 3 13 4 e DATALINK April 20 1999 DATES Program DATES changes the format of calendar dates PEDSYS Data Type D refers only to dates that are in numerical Gregorian form in order year month day without separators slash separators are added temporarily in some PEDSYS displays but are not stored as part of the date Simple conversion is typically used when an alternate calendar date representation is required for use with a foreign database Adding a constant time or age interval produces a new date at which the interval will have elapsed which is useful for setting schedules etc Introductory Display EDSYS program DATES Copyright 1992 1999 SFBR DATES changes the format of calendar dates New dates replace those selected for conversion except where constants are added to or subtracted from the original in which case they are appended as items at the end of the record Unlinked file EXAMPLE LOCUS Sub directory Enter number of the file or directory filename or Q to quit gt When the PEDSYS file containing dates to be re formatted has been selected the following dis play appears EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING Dam s Permanent ID SIRE S SEQ 9 PATERN
151. HIP SIZE 19 Mate s Permanent ID FIRST OFFSPRING SEQ 12 EGO Permanent ID 20 PEDIGREE NUMBER NE PATERNAL SIB SE 13 Birth Date YYYYMMDD 21 GENERATION NU MATERNAL SIB SE 14 Sire s Permanent ID F22 BSZ FSIBSZ FULL SIB SEQ 15 Dam s Permanent ID 16 Sex M F or U JU amp NN H ER OF OFFSPRING CALC Set precision File MASTER XMP Enter the numbers corresponding to numerical values whose precision is to be set Enter C to continue gt April 19 1999 CALC e 9 5 After items have been selected for change of precision the following display appears PSIBSZ FSIBSZ Enter desired number of digits 0 5 to the right of the decimal place gt 3 Enter R to Round number T to Truncate number gt r Here the ratio PSIBSZ FSIBSZ has been set to 3 decimal places and rounded This set of instruc tions is repeated for each variable selected When done the following instruction appears Reduce field width to length of largest number Y N zY Here the field width of all selected items is set to the minimum required to accommodate the fraction with the largest number of digits subject to numerical limits described in Appendix A Note Choice of rounding or truncating is given only for Data Type R Notes At least one operand must be a variable from the list shown
152. HOW paying particular attention to records at the beginning and the end of the file If data on the records appear to be correct go on to Step 3 If data are not correct it may be necessary to a Modify the format of records in the file using program CODE 10 December 1996 Creating a Pedigree Database 4 3 b Force records to conform to the format specified in translat cde or itemize cde by running the input file through program REFORMAT with all items selected for output c Edit records using program ALTERDAT or d Re submit the original data to program ITEMIZE Step 3 Run program INDEX specifying the Master File option choices 1 or 2 and the Unlisted Pedigree File choice When prompted enter the name of the correctly formatted version of the foreign file Step 4 Rename output files index out index cde and index mpt as MASTER lt EXT gt CODE lt EXT gt and MPOINT lt EXT gt respectively where lt EXT gt is a file extension identifying the population Output file index err may reveal inconsistencies that require correcting the original data and re running INDEX see Chapter V Step 5 Run program DBFILER to put the new Master File in DBFILES Fa Creating a linked Data File from the Keyboard In addition to the initial assumptions above creation of a linked Data File by entering data from the keyboard assumes that data are available in the form of paper records The first item in each record must be a PID ide
153. Ha CountPed b The PEDSYS Program Folder a DataLink PL Dates H DEFiler EL DelRecs Hi DownCode Bi Duplic PL GenCheck cd FoundRep CH GeneFreq GH Genotlap DEVICES bed PEDSY S settings 63 3 MB in disk CH Haplotyp H Index H Infer H temize cd Kinship Ha List H MakePed H Merge GH New Item H PedCheck LASTP ATH Ha FedTrim Ha PrePDraw H Reformat H Report H SegCheck H SetData Ha SetMastr CH Show PL ShowData HH Sibship PEDSYS RERC 168 1 ME available PL Sort Kg He Subset Ha Tally H Translat H Triplets Ha verifier CODE STD In addition to executable program files files CODE STD and DEVICES are also located in the the Macintosh PEDSYS Program Folder c PEDSYS Data Folders The example Data Folder contains the following files Example 64 1 MB in disk PATHWAY 14 items YA CODE KMP VS AMPLES CDE OP DEF ILES VA GENOMAP XMP YA MARKERS KMP VS AMPLES KMP OR RE AD ME YA DPOINTHMP MASTER KMF d Minimum System Requirements e Macintosh OS in the range 7 1 8 1 F 2 INSTALLATION and SETUP Solaris 2 5 UA MARKERS CDE TA QUANTGEN CDE Y MPOINT XMP YA QUANTGEN KMP 167 5 MB available June 10 1999 e Available hard drive space of at least 25 megabytes MB PEDSYS applications occupy about 18 MB and an additional 5 10 MB should be made available for pedigree data files depending on the size of the files and for PEDSYS applicat
154. I ER XMP to be included in Enter numbers corresponding to items in the order they ar a to set case constant C to continue to include all items Preced E to reformat item random fraction or int reformatted record justify U or L or S to insert blank to join items H to help gt En Commands Item number number with gt or lt to R J ter B K eger sequence Reordering of items within records is accomplished by entering lt n gt the number corresponding to the item in the list above the instruction line in the order that items are to appear in the output record gt lt n gt or lt lt n gt where lt n gt is an item number as described above Entry of this sequence right or left justifies the character string in the field If the justification feature is used the usual asterisk marking items chosen for inclusion will be replaced by directional markers gt marks items to be right justified lt marks items to be left justified April 19 1999 REFORMAT 35 1 U L Preceding a number with a u or 1 changes all alphabetic characters in the corresponding field to upper or lower case respectively F lt n gt where lt n gt is an item number as described above This sequence produces the following display which controls reformatting of the item selected EDNO currently width 5 Data Type I 1 Increase field width of item 2 Decreas
155. I units gt 2 2 Calculating sums etc of variables on the same record CALC makes it possible to calculate the sum count mean standard deviation and standard error of variables that appear on the same record This function is typically used to compute these statistics for multiple measurements made on the same individual when meaurements are kept on a single record per individual The function may be accessed at one of two points in program CALC s sequence of operations One opportunity to choose this function occurs when choice 2 in the Introductory Display Find sum count mean Std Dev and Std Err of items on same record has been selected the other occurs when choice 1 Calculate In log exp has been selected from the Introductory Display at which point the following display appears after the confirmation step is finished Calculate sum N mean Std Dev and Std Err of variables on the same record Y IN gt However accessed an Item List Display appears from which items may be chosen for calculations In the example below Items 15 through 27 repeated measurements of Hemoglobin Level for each indiv idual are selected The file containing these records was generated with program COMBINE which extracts items from multiple records with the same identifier and combines them on a single record April 19 1999 CALC e 9 3 Rec9 Sample Date 19 Rec5 Hemoglobin 1 Rec10 Sample Date 20 Rec6 Hemoglob
156. ILENAME gt OLD Warning Prior versions of lt FILENAME gt OLD will be deleted and over written each time DATALINK is run unless they have been renamed e Ordering Multiple entry Files It is often necessary for multiple entry data to be in a particular order for example by date of measurement To ensure that entries follow a specific order Multiple entry Files may be sorted on the critical variable such as a date with program SORT before being run with DATALINK e The last item on Linked Multiple entry Data File records is the internal pointer standard mnemonic PNTR DATALINK automatically adds this field to Data File records if it is missing as it would be prior to the first time the file is linked and adds a descriptor record to the Data Code File to reflect the change 13 2 e DATALINK April 20 1999 Files Input A Master File and a Data File lt FILENAME gt lt EXT gt named in DBFILES and their associated Code Files The Master Pointer File MPOINT lt EXT gt and Data Pointer File DPOINT lt EXT gt if the latter exists Output An updated version of DPOINT lt EXT gt is produced when the program is run and the original version of the Data Pointer File is saved as a backup under the name DPOINT OLD DPOINT OLD is not produced if DPOINT lt EXT gt is newly created An updated version of lt FILENAME gt lt EXT gt is produced if it is a Multiple entry Data File When this is done the original version of the Data
157. K KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK Fa Choice 2 3 or 4 Proband IDs read from a file A proband file is often a subset of the input pedigree file typically a Master File but may be any Data File whose records contain IDs in the appropriate form that is Permanent or Sequential Selection of a single item containing the proband ID is made from a Standard Item List Display EGO SEQUENTIAL ID 9 PATERNAL SIBSHIP SIZ Exit Date YYYYMMDD SIRE S S 10 MATERNAL SIBSHIP SIZ Exit Code DAM S SE 11 FULL SIBSHIP SIZI ate s Permanent ID FIRST OFFSPRING SEQ 12 EGO Permanent ID PEDIGREE NUMBER NEXT PATERNAL SIB SI 13 Birth Date YYYYMMDD GENERATION NUMBER EXT MATERNAL SIB SI 14 Sire s Permanent ID EXIT BIRTH I oO O1 amp NN EH N NEXT FULL SIB SEQ 15 Dam s Permanent ID N UMBER OF OFFSPRING ESTOR Identify PROBAND File MASTER XMP 16 Sex M F or U Enter a number above corresponding to Proband ID Enter C to continue gt 14 Here common ancestors of all sires in the Master File have been specified and the program pro ceeds directly to the queries described above in Choice 1 for keyboard entry of probands 6 6 ANCESTOR April 20 1999 Notes e The consequences of including ancestors for different numbers of probands can be seen from the pedi gree
158. Kids Sibs Ratio lt Label 22 gt KidSib lt Mnemonic gt Ratio lt Mnemonic gt lt Mnemonic gt lt Mnemonic gt 6 lt Width gt r lt Data type gt 2 lt Places to right of decimal point Next the source of conversion data is selected April 19 1999 NEWITEM e 29 1 A previously created conversion table may be used or a new table may b entered from the keyboard Enter S to START a new Conversion Table T to USE an existing Conversion Table Q to QUIT program STARTING a new Conversion Table When the START option is selected a Standard Item List appears EGO SEQUENTIAL ID 9 PATERNAL SIBSHIP SIZ Exit Date YYYYMMDD SIRES S 10 MATERNAL SIBSHIP SIZ Exit Code DAM S SE 11 FULL SIBSHIP SIZI ate s Permanent ID FIRST OFFSPRING SEQ 12 EGO Permanent ID PEDIGREE NUMBER NEXT PATERNAL SIB SI 13 Birth Date YYYYMMDD GENERATION NU NEXT MATERNAL SIB SI 14 Sire s Permanent ID Kids Sibs Ratio NEXT FULL SIB SEQ 15 Dam s Permanent ID NUMBER OF OFFSPRING 16 Sex M F or U I oO OFWN E EWI Items to be converted MASTER XMP After IF AND OR Enter lt Item No gt lt Operator gt lt Test gt HEN ELSE Enter lt Item No gt lt Change gt may be compound EXAMPLES IF gt 16 eq M AND gt 8 lt 9 10 11 OR gt 21 ne THEN gt 18 k3 THEN g
159. L SIBSHIP SIZ 16 Sex M F or U DAM S SE ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB S EGO Permanent ID 19 Mate s Permanent ID EXT MATERNAL SIB SI Birth Date YYYYMMDD 20 PEDIGREE NUMBE EX L SIB SEQ 14 Sire s Permanent ID 21 GENERATION NU DUPLIC Sort within groups File MASTER XMP Records will be group as marked above Optionally enter one or more numbers corresponding to items by which records will be sorted within groups precede with D for descending order Enter C to continue to next step gt In this example EGO s Birth Date Item 13 has been entered for sorting in ascending order Note that the item selected to define groups Item 19 Mate s PID is preselected in this display The within group sorting option may be skipped if the within group order of records is not critical Next the following display is shown 1 Keep single records Each item value represented by one or more records in the INPUT file is represented by a single record in duplic out Keep duplicate records Each item value represented by two or more records in the INPUT file is represented by the same records in duplic out Keep unique records Each item value represented by only one record in the INPUT file is represented b
160. LIST conventional single spaced continuous print out INELIST single spaced groups separated by blank line DASHLIST single spaced groups separated by dashed line PAGELIST single spaced groups starting on new page FORMS 3 continuous thr spaces per record FORMS 5 continuous five spaces per record PAGEFORM 3 thr spaces per record groups start on new page PAGEFORM 5 five spaces per record groups start on new page ANA O1 NN OH Select number corresponding to format of listing gt If grouped listings are selected choices 2 3 4 7 or 8 above the Item List is again displayed 26 2 LIST April 20 1999 EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING 15 Dam s Permanent ID SIRE S S 9 PATERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE 10 MATERNAL SIBSHIP SIZ 17 Exi Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 1 Code EX ERNAL SIB SI 12 EGO Permanent ID 19 Mate s Permanent ID EX ERNAL SIB SI 13 Birth Date YYYYMMDD 20 PEDIGREE NUMBE EX L STB SEQ 14 Sire s Permanent ID 21 GENERATION NU LIST Item s to define groups File MASTER XMP Enter number of one or more items to make up a key that defines record groups assumes file has been sorted on this key Enter C to continue to next step gt If PAGELIST Choice 4 has
161. Mnemonics Width Type Animal ID ID 5 C Enter label for Item 2 or RETURN for next step Note that the previouly entered Descriptor Record is shown just above the horizontal line in this display When entries for all items have been made Descriptor Records are displayed in the upper portion of the screen and a number of options are given to edit the Code File as shown below 10 2 CODE April 19 1999 Animal ID Date Necropsied Freezer Rack Tissue Box Tissue Type Quantity Health Status TH STATUS Diet 1 Oo O1 AUNE D WIN N ND OW Re OQ es Tissue Inventory to EDIT an item to ADD an item to REPLACE an item to DELETE an item to CHANGE file TITLE or S to SAVE Code File and EXIT program to QUIT program without saving Code File Command E Edit an Item Entry of e lt n gt where lt n gt is a number corresponding to one of the items to be modified produces the display shown below entry of e alone results in a request for an item number before the display appears Re enter item to right of pointer gt or enter one or more spaces to blank out item press RETURN to advance cursor or enter to go to next step gt Tissue Box lt Label 4 gt BOX lt Mnemonic lt Mnemonic lt Mnemonic lt Mnemonic gt 2 lt Width gt C lt Data type This example shows a previously entere
162. Mother Father Offspring genotypes A A A B A C B B B C C C UNKNWN TOTAL UNKNWN A B May 21 1999 SEGCHECK 37 9 37 10 SEGCHECK May 21 1999 SETDATA SETDATA is the second program of the two step process required to make batch changes to PEDSYS Data Files The program uses information from a special purpose output file named lt filename gt UPD which has been produced by program ALTERDAT Introductory Display EDSYS program SETDATA Copyright 1992 1999 SFBR ETDATA is the second program of the two step process required to make batch hanges to PEDSYS Data Files The program requires output from ALTERDAT in he form lt filename gt UPD or lt filename gt DEL where lt filename gt is the file to be modified Unlisted File EXAI PLE Enter number corresponding to the file or file group to be altered gt Confirmation Displays If changes are to made to a Data File that already exists the following display will appear when the file has been selected using the Example Marker Phenotype file as an example Data File MARKERS XMP will be updated but the file as it was before changes were made will be saved under the name MARKERS OLD In addition the update file MARKERS UPD will be renamed MARKERS OUP after the program has finished Enter C to CONTINUI x to EXIT program without updating Data F
163. NTIAL ID ER OF OFFSPRING ERNAL SIBSHIP SIZ ERNAL SIBSHIP SIZ FULL SIBSHIP SIZI EXT PATERNAL SIB SI EXT MATERNAL SIB SI L SIB SEQ EGO Permanent ID Birth Date YYYYMMDD Sire s Permanent ID 15 16 17 1 181 19 20 21 Dam s Permanent ID M F or U YYYYMMDD Sex it Date it Code ate s Permanent ID EDIGREE NUMB ENERATION NU ERG TARGET File MASTER XMP Enter number s identifying key item s on which merge will be based Enter C to continue to next step gt In the example above a single Key Item Ego PID has been selected The same Key Item is next selected for the Donor file Ego ID ADA Phenot 3 APOB Pvu2a ype 4 Tot Ser Genotype Cholestero 5 APOAI Level ERG DONOR File QUANTGEN XMP Enter number ide C to continue gt 1 ntifying key item s to next step A confirmation step follows erge will be ba EGO Permanent ID Ego ID Is this correct gt sed on in MASTER XMP TARG on which merge will be based ET file and in QUANTGEN XMP DO Y N OR file Enter If however Key Item formats do not match the following message appears details compare Enter RETURN to gt 28 2 MERGE Key Items from MASTER
164. O PID as the Key Item in the header records but leaves open the choice of PID in unlinked data records that is the PID of EGO Sire Dam or Mate etc may be designated as the Key Selection of Header Items A Standard Item List is displayed for the file from which headers are taken EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING 15 Dam s Permanent ID SIRE S S 9 PATERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE 10 MATERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB SE 12 EGO Permanent ID 19 Mate s Permanent ID EXT MATERNAL SIB SE 13 Birth Date YYYYMMDD 20 PEDIGREE NUMBER EX 1 SIB SEQ 14 Sire s Permanent ID 21 GENERATION NU RI RT Items in the header File MASTER XMP Enter numbers corresponding to HEADER items shown above in the order they ar to appear across the page Enter A to list all items C to continue to next step gt 36 2 e REPORT April 19 1999 Items will be printed in the order selected with one exception EGO Permanent ID is pre selected reflecting its designation as header Key Item and will always be printed in the left most position of the header line Standard Confirmation and Editing procedures follow If an unlinked Data File is chosen to supply header records REPORT sea
165. O Permanent ID Here PID ID069 has been entered for modification At this point ALTERDAT checks to assure first that a record for this individual can be found in the Master File If EGO is found in the Master File the program next searches for an appropriate record for EGO in the Data File If one is found the display shown below appears Note that in this case no entry appears for the APOAI Level Phenotype This is because this item is marked for hold over H which automatically erases any previous entry ID069 EDIT Record Random Order ADA Phenotype APOB Pvu2a Genotype gt Tot Ser Cholestero1 gt 103 lt APOAI Level gt lt Enter number of item to be modified S to SAVE data or X to 1 without saving data gt e Warning The carry over feature should be used with care as it is easy to inadvertently overwrite valuable information When changes have been entered and saved S for this record a new request for a PID is displayed April 20 1999 ALTERDAT e 4 3 Last entry in QUANTGEN XMP is ID077 EDIT Record Random Order Last entry SAVED was ID069 Enter to reenter changes for last entry SAVED otherwise enter individual s Permanent ID or RETURN to change mode of entry gt lt Ego ID Note that as soon as at least one record has been saved PIDs of both Last entry in lt file gt and Last entry SAVED which need not be the same are displayed A
166. OF OFFSPRING by SEX in the Example Master File export home population bdyke example MASTER XMP DISTRIBUTION OF NUMBER OF OFFSPRING BY Sex M F or U NUMBER OF OFFSPRING LIMITS LOWER 1 000000 INCLUSIVE ER 5 000000 EXCLUSIVE CLASS INTERVAL 1 0000 NUMBER OF OFFSPRING Sex M F or U lt 1 00000 2 00000 3 00000 4 00000 TOTALS 44 2 e TALLY April 19 1999 2 Distribution Parameters If the Distribution Parameters option has been selected choice 2 in the Introductory Display the following display appears EGO SEQUENTIAL ID UMBER OF OFFSPRING 15 Dam s Permanent ID SIRE S S 9 PATERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE 10 MATERNAL SIBSHIP SIZ 17 Exi Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exi Code EX ERNAL SIB SI 12 EGO Permanent ID 19 s Permanent ID EX ERNAL SIB SI 13 Birth Date YYYYMMDD 20 PED EE NUMBER EX L SIB SEQ 14 Sire s Permanent ID 21 GENERATION NUI TALLY Distribution Parameters File MASTER XMP Enter number corresponding to each item shown above for which Distribution Parameters are to be calculated For a two way classification follow this number with an asterisk and the number corresponding to the controlling variable Example 8 16 produces NKID b
167. PEDSYS A Pedigree Data Management System Version 2 0 For Sun Microsystems Unix MS Windows and Macintosh OS USER S MANUAL Draft Version July 1999 Bennett Dyke Ph D PGL Technical Report No 2 Population Genetics Laboratory Department of Genetics Southwest Foundation for Biomedical Research San Antonio Texas 78245 Programs and Manual Copyright 1989 1992 1994 1996 1999 T June 12 1999 June 12 1999 Table of Contents Note This is a draft version of the manual items marked TBA are in preparation I INTRODUCTION hentai teli leale 1 1 Il CREATING A PEDSYS DATABASE oro iel SOLA ea are 2 1 Creating a Master File from the Keyboard 2 1 Creating a Master File from Imported Computer readable Data 2 2 Creating a Linked Data File from the Keyboard 0 0 0 0 ccc eee eens 2 4 Creating a Linked Data File from Imported Computer readable Data 2 4 Creating an unlinked Data File from the Keyboard 2 6 Creating an unlinked Data File from Imported Computer readable Data 2 6 I cPEDSYS Programs uc Roli eps ed ail tothe et ns fu ne kh karen Rail ten eat Ge 3 1 PERINI as de Sn dete tata Meant aera Sates rn etd 3 3 ALTERDAT pitira ate ILA Araceae oe nae areas NI 4 1 ALTMASIR ess ne Ovals aim Aas aida 5 1 ANCESTOR ER rente Pines a 6 1 a allot Beet awe earn A a ae E ta pedi 7
168. PLE LOCUS Sub directory Enter number file name or Q to quit gt When the PEDSYS file has been selected that contains items to be checked for duplication the following display appears EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING 15 Dam s Permanent ID SIRE S SEQ 9 PATERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SI 10 MATERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exit Code EX ERNAL SIB SI 12 EGO Permanent ID 19 Mate s Permanent ID EX ERNAL SIB SI 13 Birth Date YYYYMMDD 20 PEDIGREE NUMBE EX 1 SIB SEQ 14 Sire s Permanent ID 21 GENERATION NU DUPLIC Select grouping criteria File MASTER XMP Enter one or more numbers corresponding to key items by which records will be grouped or C to continue gt Here we have chosen Mate s Permanent ID as the single item for comparison Records in the input file will be grouped on the basis of this item prior to checking for duplication e Option Sorting Duplicate Records It is sometimes useful to order records containing duplicate entries An opportunity to do this is provided in the next display which allows records to be sorted within groups of duplicates April 20 1999 DUPLIC 18 1 EGO SEQUENTIAL ID ER OF OFFSPRING 15 Dam s Permanent ID SIRE S S ERNA
169. Permanent ID SIRE S S 9 PATERNAL SIBSHIP SIZ Sex M F or U DAM S SE 10 MATERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB SI 12 EGO Permanent ID 19 Mate s Permanent ID EXT MATERNAL SIB SI 13 Birth Date YYYYMMD 20 PEDIGREE NUMBER EX 1 SIB SEQ 14 Sire s Permanent ID 21 GENERATION NU TALLY Frequency Distribution File MASTER XI Enter number corresponding to each item shown above for which a Frequency Distribution is to be calculated For a two way classification follow this number with an asterisk and the number corresponding to the controlling variable Example 8 16 produces an NKID by SEX column by row distribution for a Master file Enter C to continue to next step gt April 19 1999 TALLY e 44 1 Here a two way classification of NUMBER OF OFFSPRING the tabulated variable by SEX the controlling variable has been selected Since the tabulated variable is numeric the following sequence appears after the Standard Confirmation and Editing step Set bounds on the value of NUMBER OF OFFSPRING for which a Frequency Distribution is calculated Y N gt y Enter INCLUSIVE lower bound for value of NUMBER OF OFFSPRING Values below this bound will be tallied as a single class Enter RETURN alone to
170. R checks type C ters fields may also contain a single decimal point is checked to verify that field widths of EGO SIRE 3 32 characters same EDSYS program V character fields contain only printable characters contain only numbers isplay ERIFI 1999 SFBR ER Copyright 1992 to verify that all fields contain entries consistent with their or D date fields contain only integers 3 4 7 or 8 charac numerical fields and one leading or real number a Master File and DAM PID s are the birth date is earlier than exit date and SEX field I R leading blanks In addition contains only 1 2 3 M F U or m f u Unlinked File EXAI PLE LOCUS Sub directory Enter the gt number of the file or directory to use When RETURN is pressed a Standard File List Display appears Error Messages File verifier tab contains the name of the file that was tested with its accompanying Code File identifies each record and field in which an error occurs and gives a description of the error Note The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example verifier subset out Files Input Any Master File or Data File with an accompanying Code File If the file to be verified is a Master File CODE STD is required Output June 5 1999 verifier
171. RIS 2 5 E 5 Before PEDSYS can be used an Input Data Directory must be selected and attached to the programs and the output directed appropriately Input and output directories may be set in several ways but the most convenient is to use program setpath which is started by entering the command setpath from any directory which results in the following display from which Input and Output Directories may be selected At the top of the screen is a list of directories to which input and or output paths may be changed This list always includes the Current Working Directory and the Other Unlisted directory Additional Input Data Directories are read from the setpath directory file DBDIRECT described below The example directory is the only Data Directory that has so far been added to the directory list 1 Current 2 Other Unlisted 3 EXAMPLE Enter Input Data Directory number 1 26 O to change the Output Directory A to add a new directory D to delete a directory H for help or O to quit gt 3 Current Working Directory home users bdyke Output Directory home users bdyke Input Data Directory home users bdyke At the bottom of the screen are listed paths to three directories Current Working Directory is the one that the user is accessing at the moment that is the one from which the PEDSYS shell has been invoked This directory is fixed once PEDSYS programs have been started and may be change
172. RT and SUBSET which were designed for human population studies In 1981 I moved to the Southwest Foundation for Biomedical Research The basic PEDSYS record structure as well as these four programs were modified for use with non human animal populations and the linked pointer file structure was developed with the help of Ms Linda J Collins Ms Collins implemented the file structure and took major responsibility for PEDSYS programming and devel opment over the next five years with the assistance of Ms M Connie Murguia Ms Collins original work underlies much of the subsequent development of PEDSYS Dr Jean W MacCluer has played a major role in the overall planning and development of the package and has made numerous suggestions for new functions and improvements A number of programs are based on her original algorithms In 1987 Ms Linda Freeman Shade became lead programmer for the package She did most of the conversion of the FORTRAN code first for MS DOS and then for Sun Microsystems Unix In addition to these demanding tasks Ms Freeman Shade has made important progress in algorithm development and implementation for many of the Pedigree Management Programs Much of the success of the package is the result of her programming skill understanding of the objectives of pedigree management and an extraordinary talent for making complex tasks simple to carry out Ms Rose H King contributed substantially to algorithm and program deve
173. ST computes the number of characters required to print a record from information taken from the Code File Specifically this is the sum of the field length parameter or the width of largest mnemonic minimum 4 maximum 6 characters whichever is longer plus a single blank space per item for all items selected for listing This number is then compared with the printer line length parameters in file DEVICES see The Device Control File Appendix A to determine the largest type size that can be used to print the full line If the number of characters is too great to be printed on a single line using the smallest available font a warning message appears with a request to reduce the number of items to be printed see Output Width Adjustment above The number of lines that can be printed on a single page is variable but we have found that 50 records on an 11 inch long page in continuous single spaced format is convenient With number of records set at 50 in the DEVICES file FORMS 3 format gives 17 records per page and the larger FORMS 5 boxes permit 11 records per page Files Input Any Master File or Data File and an associated Code File The Device Control File DEVICES Output Printer console screen or output file list tab Records selected from the input file will be printed in their original order Fa April 20 1999 LIST 26 5 26 6 LIST April 20 1999 MAKEPED Program MAKEPED constructs pedigrees connecting one or mo
174. Specifying the Validity of Data Entries The PEDTRIM default is to trim individuals from a pedigree when data are missing from their records However there are two situations in which this convention may require modification 1 The PEDSYS convention of representing missing data as a field of blank characters can poten tially lead PEDTRIM to remove the wrong individuals from a pedigree For example an attempt to restrict membership of a pedigree to living individuals requires that records contain ing blank death date entries be retained since a blank death date implies that the individual is still living 2 Some non blank data items may consist of values that are known to be unacceptable For exam ple serum samples used to determine marker phenotypes are often designated Unt if they are untypable for some technical reason Clearly an individual labeled this way is a candidate for removal even though the field is not filled with blanks The next operation makes it possible to override the simple missing data default criterion for removal and to specify alternate data values that are unacceptable making the individual bearing them a candidate for trimming 32 4 PEDTRIM July 8 1999 1 ADA Phenotype 3 CA1 Phenotype 4 G6PD Phenotype 2 APOB Pvu2a Genotype PEDTRIM Redefine exclusions Enter numbers corresponding to items for which the default missing data criterion for exclusion from the pedigree is to be overriden E
175. TR adds Sequential ID numbers and other items to the basic information and creates a functional Master File formatted as shown in the table below The ALTMASTR SETMASTR sequence is also used to update pre existing Master Files e An ASCII text file of individual records each containing at minimum a unique PID for Ego and Ego s parents and a code designating sex may be transformed into Master File format Some pre processing may be required if records are incorrectly coded or formatted or contain items that more appropriately belong in a Data File Program INDEX and adherence to the conventions of the CODE STD file provide guides to data preparation for Master Files Most programs require that Master Files be named MASTER lt EXT gt where lt EXT gt is an extension identifying the population For example MASTER XMP is the name of the Example Master File distributed with the PEDSYS package Twenty standard items of a Master File are formatted as shown below Notes on Master File Record Format e Mnemonics are invariant although allowances are made for differences between human and non human genealogical terminology father vs sire etc e Items 1 12 are fixed in position Items 1 11 16 19 and 20 are invariant in length e Items 12 14 15 Maximum length of Permanent IDs may range from 3 to 9 characters but must be the same in all records of a given Master File Actual length of entry may not exceed length specified in
176. This contrasts with the 12 items of only 15 records that result from the 80 column by 34 row setting used for illustrations in this manual See Chapter II Setup and Installation for details on these capabilities 8 6 BROWSE April 19 1999 6661 61 dy L 8 e ASMOUA E gt MASTER XMP 1 SEQ L I o O1 amp N H LO J O U1 NH 20 21 22 23 24 25 26 27 28 29 30 31 32 nter 1 21 2 SSEQ Have NWO 000 0000 0 RR oo 3 1 D L NN RN BU BOOCOOOOOOO Items 4 5 6 7 8 FSIB NK o 050 DOO OD DD DD OAS OO OSS Oo 0 a o 05 OO DD DD DD DODDDONNODAKHLAWOOKW WwW oo Po OS O0O0OS O0 Oooo 00 00 TOD oo DD DO ODDO lt n gt or lt n gt for new page PID S lt n gt to set window L to lock columns to 21 Top record 1 32 9 10 11 12 D PSIBSZ MSIBSZ FSIBSZ ID DO61 D056 D038 D04 CO mie ze ou D04 DO NOD DOO DODO UU DO D06 D03 D015 D068 D054 D070 D077 D067 D07 D049 D069 D095 D11 D097 D080 D083 D103 D109 DLT D124 D130 SUUNWWIKIUNUAN DSSNNEb5b5IN NN Pe PPS Ooo OOF KEMAHLI NEA DO oc 60 066 PNY SO OO OOF NRE Wh NB DO 00000066 CPP ME Ee eee oor SO Bee Ee ona Oc 13 BIRTH 972 03 09 973 12 23 974 05 05 975 00 00 977 10 29 979 00 00 980 03 10 982 00 00 988 02 11 980 11 28 982 00 00 981 07 05 987 06 23 987 00 00
177. UNTPED designates a family identification number The program makes it possible to assign an alternate family identification number if the standard PEDSYS mnemonic is not found The program next compares the Code File of the input file with entries in CODE STD for standard mnemonics identifying Ego and Ego s parents CRI MAP requires Sequential IDs see below but some latitude is provided in designating IDs for FISHER MENDEL S A G E REGC and LINKAGE where the following sequence appears if the Code File contains standard PEDSYS mnemonics for both Permanent and Sequential IDs Conversion to this format requires the presence of IDs for EGO FA and MO on each input record Enter RETURN to use Permanent IDs or S for Sequential IDs Enter O for selection of other IDs that might not be labeled with PEDSYS standard mnemonics O to quit without executing gt Notes on pedigree analysis conversions e A Phenotype Genotype Map need not be created for autosomal codominant loci that adhere to the conventions listed in Appendix C Rules for Genotype and Phenotype Nomenclature Nonetheless is it frequently helpful to generate a map for autosomal codominant loci because TRANSLAT will otherwise be forced to read through the entire Data File twice for each locus once to tally phenotypes and again to do its conversions Presence of a map file eliminates the need for the tallying step and can significantly speed exec
178. UTION GENEFREQ uses a simple counting procedure to calculate gene frequencies and is subject to limitations described in the EDSYS User s Manual Appendix A Unlinked File merge out Example LOCUS Sub directory Enter number of the file or directory to use gt 4 Loci may be selected for analysis in several ways 1 An unlinked file containing genotypes or phenotypes for one or more loci It is often convenient to organize multiple genotypes and or phenotypes on the same record An ex ample of this organization is given by file merge out choice 2 above in which genotypes for three loci have been assembled on records for each individual display from program BROWSE out Top record 1 32 2 3 4 5 DIS DIS D2S SAMPLE 1656 515 1329 NUMBE W236 W240 W238 W216 W218 W230 W232 ID015 B ID019 B 1D034 A ID038 A C B B U BB AA AC AC AC BD AB Q io BB 1D042 1D045 ID047 tr D B Wwe GI Enter lt n gt or lt n gt for new page lt n gt 1 32 to set top row gt or lt lt n gt to shift window I lt n gt 1 5 to set window L to lock columns T to change instructions N for new file F to find H for help Q to quit gt When an unlinked file of this type is selected the following display appears from which loci are selected for analysis April 20 1999 GENEFREO e 20 1 1 EGO Permanent ID 3 D1S515 Genotypes 5 Sample No 2
179. _root bin This makes it possible to run PEDSYS from any working directory To see the program menu enter the command pedsys The first time this command is issued program setpath is run see below from which the Example directory should be selected for input The PEDSYS program menu is then displayed e Note Executable program files currently require over 85Mb of disk storage on the Sun SPARC Station exclusive of data requirements a 3 Unix File Access and Permissions Since Unix is a multi user operating system issues of access and security are complex and require careful implementation In general the strategy is to control access and security by assigning standard Unix file permissions to the various files and directories File permissions are denoted by a 10 charac ter Permissions Field that appears at the beginning of each file descriptor record This field can be seen by displaying the contents of a directory in long format that is by entering Unix command 1s 1 The first character of the field will be either the letter d indicating that the descriptor record applies to a directory or a dash indicating that record describes a file The next nine characters fall into three sets the first of which specifies permissions given to the owner of the file or directory The second and third sets specify permissions for a group of users and the world all other users respectively Permissions within each set are orde
180. a good idea to consider the use of a shell script see Appendix E so that the commands necessary to produce the report are stored for repeated use Only one unlinked Data File may be used as a source for data records The command line shortcut with two input files program name followed by a blank header filename another blank and the data filename may be used to start this program Example report sort out subset out Files Input Header A Master File or Data File with Code File in which each records carries a PID Data One or more Data Files usually multiple entry and their associated Code Files The Device Control File DEVICES Output Printer console screen or disk file report tab An example of REPORT output is given below HEADER FILE MASTER XMP 15 Mar 1999 DATA FILE S QUANTGEN XMP HEMOGLOB XMP BIRTH F EXIT 1972 03 09 1998 04 20 1 DATE 1982 03 24 1983 01 12 1984 10 04 1985 10 15 April 19 1999 REPORT 36 5 REPORT output example continued 1986 10 06 1987 06 10 1988 04 15 1989 04 14 1990 01 15 1992 01 10 1993 01 13 1994 01 20 1995 01 24 JO OO DW I CO e SIN N HS BIRTH 1973 12 23 APOB Pvu2 GENO TYPE A2A2 104 115 3 DATE 1982 05 10 1983 09 21 1984 10 02 1985 11 04 1986 11 06 1987 10 27 1988 10 12 1989 09 12
181. a subset of items enter L To switch cyclically from one LINKED file to the next enter If files have not been preselected initial entry of presents a File List from which they may be chosen Enter W to write a record to output file SHOW lt n gt OUT Press RETURN to continue gt Q Exits the program Fart Row locking By default items in the record are displayed from top to bottom of the screen in their original order This default may be overridden so that some items may retain a fixed position on the screen Entry of L produces the following Item List Display EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING 15 Dam s Permanent ID SIRE S SEQ 9 PATERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SI 10 MATERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB S EGO Permanent ID ELD s Permanent ID EXT MATERNAL SIB SI Birth Date YYYYMMDD 20 PEDIGREE NUMBER EXT FULL SIB SEQ Sire s Permanent ID 21 GENERATION NU SHOW File MASTER XMP Enter numbers corresponding to items shown above in the order they are to appear from top to bottom of screen Enter C to continue gt In the example above Items 12 through 19 have been allocated to locked rows using common spreadsheet terminology sta
182. ab results can be output in PEDSYS format and sent to files tally lt n gt out and tally lt n gt cde where lt n gt is the order that variables are selected for computation Write results to output files in PEDSYS format Y N gt Output Example PEDSYS format Below is an display of file tallyl out showing the frequency distribution specified for NUMBER OF OFFSPRING by SEX in the Example Master File output of program BROWSE 44 4 e TALLY April 19 1999 tallyl out Items 8 Top record 1 2 1 2 3 4 5 6 7 8 SEX NKID NKID NKID NKID NKID NKID NKID lt 1 0000 2 0000 3 0000 4 0000 gt TOTAL F 5 17 M 2 9 LS Enter lt n gt or lt n gt for new page lt n gt 1 2 to set top row gt or lt lt n gt to shift window I lt n gt 1 8 to set window L to lock columns N for new file F to find H for help Q to quit gt Notes e Integer data are converted to real floating point numbers if bounds are set This change will be preserved in column and row headings in tally tab Conversion of integer to real is not done if bounds are not required e Output is formatted as F12 4 giving a range of 0 0001 through 9999999 9999 in absolute value Internal computations are done in double precision floating point arithmetic see Appendix A page A 3 for specifications e Blank fields are treated as missing data rather than as zeros in calculations of Distribution Parameters e The
183. accessed automatically from file subset out which in this example contains records for individuals ID049 and ID069 Altogether six coefficients are calculated kinship out Top record 1 6 1 2 3 4 SEQL SEQ2 IDI ID2 17 18 IDO71 ID049 250000000 17 19 IDO71 ID069 039062500 20 18 ID067 ID049 000000000 20 19 ID067 ID069 062500000 11 18 ID045 ID049 250000000 11 19 ID045 ID069 000000000 Enter lt n gt or lt n gt for new page lt n gt 1 4 to set top row gt or lt lt n gt to shift window I lt n gt 1 5 to set window L to lock columns T to change instructions N for new file F to find H for help X to exit gt 25 6 KINSHIP April 20 1999 Notes e KINSHIP requires that records of parents appear prior to those of their offspring in the input file Master Files and pedigree files produced by program INDEX meet this requirement It is a good idea to run INDEX on a pedigree file if there is any doubt about the order of its records The Master Pointer File option in INDEX is required in this case e The Stevens Boyce algorithm uses a path searching method based on the relationship l f d f i l where fis the inbreeding coefficient of an individual l is the number of loops of relationship formed by following paths to and from Ego and an ancestor common to both parents and n is the number of individuals in each loop excluding Ego e The Quaas Henderson algorithm depends
184. ade to MASTER lt EXT gt Presence of original Update Files results in the following error message on the screen after entry of the password WARNING UPDATE lt ext gt or DELETE lt ext gt already exists Program SETMASTR or ELRECS has not been run successfully since the last time ALTMASTR was used you continue without running SETMASTR or DELRECS first the contents of PDATE lt ext gt or DELETE lt ext gt will be destroyed Enter C to CONTINUE or X to EXIT program gt e SETMASTR should be run before running DELRECS Output File UPDATE lt EXT gt contains the following information PDATE PID gt lt mnel gt lt mne2 gt lt mne3 gt lt mne4 gt lt newvalue gt PDATE PID gt lt mnel gt lt mne2 gt lt mne3 gt lt mne4 gt lt newvalue gt EW ENTRY PID gt lt iteml gt lt item2 gt lt itemn gt where records containing the words UPDATE and NEW ENTRY indicate the type of change represented in the record immediately following An UPDATE record begins with the PID of the Master File record to be changed This is followed by all four mnemonic words identifying the item and the new value to be added or substituted A NEW ENTRY record begins with a PID followed by values of all items in the order they are to be included in the record File DELETE lt EXT gt contains only PIDs of records to be deleted
185. aken to observe format requirements Although the label contained in the first Label Record may be the full 54 characters long a limit of about half this length is preferred This label may be the file name or preferably a more descriptive title Subsequent Descriptor Records are formatted as follows Key Start Format I2 1X A21 4 1X A6 1X A1 June 12 1999 APPENDIX A e A 7 Where represents a character in a field read by PEDSYS programs o represents a single blank used as a visual separator ignored by PEDSYS programs is a visual marker pointing to the first character in each field Numbers below this marker represent the starting column of each field Notes on Code File Record Format a The first field in the Descriptor Record columns 1 2 contains the field length of the data item b The second field is an Item Label columns 4 24 containing a description of the data that is used in screen and print display Program operation is not affected if the field is left blank c The next four fields columns 26 31 33 38 40 45 47 52 contain item mnemonic words Mnemonics are used by PEDSYS programs to locate standard items in records and as labels in printed listings In some cases the mnemonic words are specified explicitly see a The Master Code File and d Code Files for Genetic Marker Data Files below Otherwise other mnemonics may be chosen arbitrarily with the restriction that the first mnemonic word should n
186. al PID for EGO or lt kid1 gt then re enter change of EGO s BIRTH If b first change assignment of lt kid1 gt s parent in the Master File then re enter change of EGO s BIRTH In all cases use ALTMASTR in ALTER mode and re run SETMASTR using the most recent Update and Master files see note on renaming and deleting these files Notes e lt ego gt refers above to the PID of EGO as it was entered in the UPDATE lt EXT gt file 39 6 SETMASTR April 20 1999 e In rare circumstances it may be easier to correct SETMASTR errors by repeating an update session using the previous input files This may require deleting the newly created MASTER lt EXT gt MPOINT lt EXT gt and DPOINT lt EXT gt files renaming MASTER OLD to MASTER lt EXT gt and reconstituting the previous MPOINT lt EXT gt and DPOINT lt EXT gt e The number of each error appears in parentheses at the end of the error record Files Input Output Any Master File and its associated Code File and Master Pointer File UPDATE lt EXT gt produced by program ALTMASTR containing changes or additions to Master File records DPOINT lt EXT gt is required if new records are added to an existing Master File to which Data Files have already been linked MASTER lt EXT gt is the new or updated Master File produced by the program MASTER OLD is a backup copy of the input Master File produced if MASTER lt EXT gt is generated as the result of changes and or a
187. allying step and can significantly speed execution If a Phenotype Genotype Map File is found and it contains the selected phenotype an alternate display appears ENOMAP XMP contains entries for ABO PHENO TYPE AUDR Enter RETURN to use GENOMAP XMP Otherwis nter name of alternate genotype phenotype map file loci not listed in a map file are assumed to be autosomal co dominant gt In some cases genotypes or phenotypes can be inferred from the types of other family members see program INFER Control over inclusion or exclusion of inferred types in gene frequency calculations is given in the next instruction 20 2 GENEFREQ April 20 1999 INFERRED alleles and genotypes are designated by enclosure in parentheses Enter E to EXCLUDE inferred types in allele frequency calculations I to INCLUDE inferred types in allele frequency calculations When this choice has been made the program begins execution a 2 A single locus chosen from the LOCUS Sub directory When the LOCUS Sub directory is selected choice 4 in the Introductory Display the following display showing all files listed in its Directory File DBFILES appears AllLoci CandLoci D1S1656 D1S515 D2S1329 D2S326 D3S1229 D4S1582 D5S1466 D6S1036 e D7823 GGAT1A4 s E o a O1 amp NN H APOBpvu2a CA1 ErrorDemo G6PD Enter a file n
188. alue R for real value C for character value April 19 1999 CODE e 10 1 These requests are in order a b The item name or description 21 characters maximum Up to four mnemonic words describing the item maximum 6 characters each These should be chosen carefully as they are used as column headings for the output of program LIST and may serve as the only convenient means of identifying data presented in long listings It is important that no two items have exactly the same mnemonics Completion of entry of the fourth word results in a jump to the next class of requests that is to c below but all four mnemonics need not be entered a carriage return alone also results in a jump to the next request Field length of the item 1 99 An error message will result if an appropriate numerical value is not entered here Data type of the item I R C and D An error message will result if an appropriate letter is not entered here Type D date is permitted only if field width is 3 4 7 or 8 corresponding to date formats YYY YYYY YYYMMDD or YYYYMMDD Once data type has been entered the Descriptor Record is displayed at the top of the screen and an opportunity is provided to make changes in it by shifting to Edit Mode 5 Animal ID Edit this item Y N gt If the Edit option is not selected the choice of entering the next Descriptor Record or of leaving Create Mode is given Item 1 Label
189. ame or by double clicking a PEDSYS data file from the DeskTop This editor is based on the text editing routines provided by the Macintosh Toolbox and thus cannot accommodate all the data in a file containing more than 32 000 characters If such a file is opened the first 32 000 characters are loaded and a warning message is displayed In these circumstances if the file is saved under the same name the contents of the original file beyond 32 000 characters will be lost The text face and size are taken from the PedSys Font menu settings Printing When generating printed output with List Report or Tally the standard Macintosh Print dialog is presented allowing standard printer options to be set before anything is actually printed Any compatible printer selected through the Chooser or attached as a serial port device may be used The amount of text printed on a single page is governed by the page orientation portrait or landscape and the reduction enlargement 25 300 values which may be set in the Page Setup dialog when the program is started The greater the reduction the more text is printed per page Text is printed in the size and font selected from the Font menu subject to the specified reduction enlargement value For example a text size of 12 printed at 25 would yield printed text of size 4 which is quite readable when printed at resolutions of 600 DPI or more Mousing Around In a modest effort to provide a little of the
190. amp a2L lt 027 gt s0p16 6h8 5v0s 1b0T lt 012 gt 4 Number of Devices lpl 4 OTC Line Printer 136 050 lt 018 gt lt 027 gt lt 080 gt 162 050 lt 018 gt lt 027 gt lt 077 gt 226 050 lt 015 gt lt 027 gt lt 080 gt 247 050 lt 015 gt lt 027 gt lt 077 gt lt 018 gt HP1 HP Laserjet III 27 gt amp 100 lt 027 gt 8U lt 027 gt amp a2L lt 027 gt s0p10h12v0s0b3T 27 gt amp 1108D lt 027 gt 8U lt 027 gt amp a2L lt 027 gt s0p16 6h8 5v0s 1b0T 4 Sun LaserWriter usr local bin nenscript R B L64 usr local bin nenscript lr B fCourier9 L54 usr local bin nenscript lr B fCourier Bold8 L60 June 12 1999 APPENDIX A e A 17 166 064 usr local bin nenscript lr B fCourier Bold7 L64 lt 000 gt CON 1 Console Screen 080 014 lt 000 gt lt 000 gt 12 Note that the line printer and console codes are similar to those in the MS DOS Epson configuration shown above but those for the HP LaserJet and the Sun LaserWriter are quite different The LaserJet uses HP Printer Control Language sequences which can be found in the User s Manual accompanying any Hewlett Packard printer The LaserWriter uses PostScript control sequences which are provided by nenscript a public domain Postscript translation utility described in Appendix D The Device Control File provided for the Macintosh computer appears as follows 2 MAC 1 Macintosh pri
191. an individual in the Master File lt n gt lt n gt The command behaves exactly the same for both Linked and unlinked files that is entry of or followed by an integer displays records belonging to the individual lt n gt records from the last one currently selected for display FilePos The default value of lt n gt is 1 so that entry of alone advances the display by one record In case of unlinked files however this command has a more predictable result because records are ordered sequentially by ID RETURN As in the case of Linked Data Files entry of RETURN alone advances the display to the record immediately following the last record currently displayed Since unlinked files are ordered this command makes it possible to step through the file sequentially individual by individual se Column locking By default all items in the record may appear in the display window in their original order depending on the position of the window with respect to the record This default may be overridden so that some items may retain a fixed position in the window Entry of L produces the following Item List Display 1 Animal ID 4 Vial Type 7 Project Code 2 Sample Number 5 Sample Status 8 Comments 3 Date Taken 6 Animal Status 9 INTERNAL POINTE SHOWDATA File SAMPLES XMP Enter numbers corresponding to items shown above in the order they are to b assigned to locked left hand columns or
192. an unlinked pedigree file has been selected initially Once input data files have been selected construction of a Pedigree Draw file involves a series of steps in which 1 a Symbol Selection Table is specified 2 items to appear as text fields in the the Pedigree Draw diagram are specified 3 symbol types and attributes are selected from standard Pedigree Draw palettes 4 the Symbol Selection Table may be modified optionally and 5 individuals to be included in the output are selected Step 1 Specifying a Symbol Selection Table The Symbol Selection Table collects the sequence of text and symbol selections as they are entered during the operation of PREPDRAW Once created this table which is distinct from the Symbol Palettes described below may be edited during any run of the program as described in Step 4 below The table also may be saved and reused so that new Pedigree Draw files can be created from the same May 4 1999 PREPDRAW e 34 1 PEDSYS files without having to repeat an entire symbol selection sequence When files have been chosen the following display appears from which the source of a Symbol Selection Table may be chosen A previously created table of pedigr text and symbol selections may be used or a new table may b ntered from the keyboard Enter S to START a new Symbol Selection Table T to USE an existing Symbol Selection Table Q to QUIT program In the example above creation of a new table
193. and the beagles direc tory will be listed in the setpath display c Deleting Directories from DBDIRECT Directories may be deleted from file DBDIRECT by entering d at the initial setpath prompt which produces the following display showing the beagles directory added above 1 Current 2 Other Unlisted 3 EXAMPLE 4 BEAGLES Enter the number of the directory to be deleted or press RETURN to cancel gt 4 Here a 4 has been entered which will delete the pedsys beagles path from file DBDIRECT and remove the beagles name from the setpath list of directories Notes e The operation of setpath creates or modifies a file named PATHWAY in the Current Working Directory PATHWAY contains either one or two records the first of which is always the path to the Input Data Directory The second record if it is present contains the path to an Output Directory If a second record is not present output is automatically directed to the Current Working June 10 1999 INSTALLATION and SETUP SOLARIS 2 5 E 7 Directory An example of records in a PATHWAY file might be pedsys example home users bdyke temp Here the example directory has been selected for input while output will be sent to the subdirectory named temp Both input and output data bypass the Current Working Directory in this case e Program setpath modifies the PATHWAY file if one is present in the Current Working Directory otherw
194. as number of days e Gregorian and Julian forms may not be mixed except to the extent that representing the partial year as number of days since 1 January month code J may be thought of as Julian July 7 1999 DATES e 14 5 Year month and day may be separated by a period dash comma forward slash or a blank Any of these characters may be followed by a single additional blank PEDSYS date format does not permit the use of separators If separators are inserted the resulting output will be designated as Data Type C rather than Data Type D in a PEDSYS file Blank or zero date fields in the input file are output as blank fields in output file dates out A full eight digit field of 9s or UNK or unk appearing in the first three characters of the field represent ing unknown dates in the input file will be left unchanged in the output file If output format specifies more date elements than appear in input fields the trailing portion of the output date will be filled with zeros if output is all numerical or blanks if alphabetic month is specified Examples are shown in the table below where the result of converting incomplete or abridged input dates to a more complete format is given Output format specified Form of input date month dd yyyy YYYY MM DD 19910100 or 1991Jan00 January 00 1991 1991 01 00 19910000 or 1991 1991 1991 00 00 etei A constant day and or month cannot be added or subtracted from an abridged inpu
195. ast one a or b allele is known when phenotype A or B respectively is found The latter case is designated by a single allele symbol fol lowed by a dash where the dash indicates that the second allele has as yet not been determined INFER starts with this information and iteratively attempts to replace missing types according to the Mendelian laws as illustrated in the next diagram April 20 1999 INFER e 23 7 ID070 AB ab Pedigree DrAw As before inferred allele types genotypes and or phenotypes are surrounded by parentheses In this pedigree it has been possible to infer complete genotypes for all but two individuals 1D038 and ID077 Example 3 Inferring X linked Phenotypes A Phenotype Genotype Map is required for correct inferences to be made for X linked phenotypes INFER proceeds by assigning genotypes on an a priori basis as illustrated in the diagram below 23 8 e INFER April 20 1999 ID038 ID056 A Es 1D077 ID070 ID054 AB B B ab bb bY Pedigree DrAw Directly below each individual s PID is shown the G6PD phenotype exactly as it appears in the G6PD locus file Note that there is no entry for individuals ID015 ID045 ID056 ID067 or ID068 Be low each phenotype is an a priori genotype assignment many genotypes can be deduced unambiguously since phenotypes are codominant in females and hemizygous in males The symbol Y has been assigned to designate the Y chromosome in males This has been paired wit
196. at for Master Files and unlinked Data Files the and S commands are interchangeable gt lt i gt or lt lt I gt where lt i gt is an integer in the range 1 through lt nitems gt the number of items on the record Entry of this sequence shifts the unlocked portion of the window horizontally by lt i gt items without changing page position In the example above 1 lt lt i gt lt 21 since there are 21 items per record in the Example Master File I lt I gt where lt i gt is an integer in the range 1 through lt nitems gt the number of of items on the record Entry of this sequence sets the horizontal position of the item selected at the left most unlocked 8 2 BROWSE April 19 1999 N column In the example above 1 lt lt i gt lt 21 since there are 21 items per record in the Example Master File Entry of this command makes it possible to lock columns that is fix their position so that they remain visible despite horizontal shifts of unlocked items in the display window See explanation of column locking below This command makes it possible to switch the BROWSE record display rapidly between linked files selected when the program is started Entry of an asterisk switches the display cyclically to one of the selected files If an individual has been chosen explicitly by entry of either PID or SEQ in one linked file the top record of each of these displays will belong to the same individual providing that there is
197. ata Files 1 Unlinked File EXAI PLE LOCUS Sub directory Enter number or name of file TO which data will be added O to quit 32 A Standard File List appears next with an instruction for selecting the Target file Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Enter number of TARGET file TO which data will be added gt 1 Here the Example Master File has been selected Note that the Target file need not be a Master File in fact records from any two files may be merged so long as they have the same Merge Key Item format see Selecting Key Items below The procedure for selecting the Donor file follows the same pattern as described above Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Enter number of DONOR file FROM which data will be copied gt 2 In this example the Markers Quant P types file will be merged to the Example Master File Selection of Key Items that govern matching of records in the two files is done next April 19 1999 MERGE e 28 1 Selecting Key Items Records are merged only when each contains an identical Merge Key Merge Keys consist of one or more Data Items selected from Standard Item Lists that define records of both the Target and the Donor files The Target file Item List appears first EGO SEQ SIRE S S DAM S SE FIRST OFFSPRING SEQ E
198. ata err contains a record and diagnosis of changes that were attempted but were unsuccessfully completed because of an error or inconsistency detected by the program DPOINT lt EXT gt the Data Pointer File is written when the Data File is updated This will be a modified version of the previously created file DPOINT OLD is a backup copy of the previous version of DPOINT lt EXT gt irs 38 4 e SETDATA April 20 1999 SETMASTR SETMASTR is a second program of the two step process required to make changes in Master Files The program uses information from a special purpose output file named UPDATE lt EXT gt which has been produced by program ALTMASTR Introductory Display EDSYS progr SETMASTR upd am SETMASTR Copyright 1992 1999 SFBR ates Master Files from changes stored in the special purpos output file UPDATE lt ext gt produced by program ALTMASTR The following ed as input to the program files are us CODE lt ext gt UPDATE lt ext MASTER lt ex MPOINT lt ex DPOINT lt ex to which D Enter C S Q Commands C Changing an exis always required required if changes are made to an existing Master File LU n t gt is required if new records are added to a Master File ata Files have already been linked to make CHANGES to an existing Master File to START new Master File to QUIT program ting Master File Changing a preexis
199. ate a Master Pointer file Y N gt The Master Pointer File is an important component of the PEDSYS file system and must be created if a Master File is being created for the first time In fact however it is usually a good idea to create a new Master Pointer File any time INDEX is used to create a Master File Choice 2 Master File with additional indexed individual Choice 2 also creates a standard PEDSYS Master File but adds an index for another individual appearing on Ego s record This feature may be used to create Sequential IDs of mates usually for monogamous species or single pair caging The command sequence is the same as for Choice 1 except that the following Item List Display appears after file selection a pedigree file examped has been created for this example EGO Permanent ID 4 Dam s Permanent ID Exit Code Birth Date YYYYM 5 Sex M F or U ate s Permanent ID Sire s Permanent I 6 Exit Date YYYYMMDD INDE File examped Individuals marked with an asterisk will be indexed and the first eleven items above replaced To index an individual other than EGO FA or MO enter the corresponding number above Enter C to continue to next step gt 8 EGO FA and MO are pre selected and another individual may be indexed in which case a new Sequential ID will be inserted just after the individual selected Here Mate s PID has been selected for indexing Subsequent queries
200. ate function is similar to the hold over feature Commands H and HA and the Duplicate feature Command D available when selecting items for modification in that it can eliminate the need to re enter identical information on more than one record during a session There are however some subtle differences between the three functions Hold over Duplicate Command D Template Command H EDIT Mode only Command T File type affected Single and Multiple entry Multiple entry Multiple entry only only Records affected Any record saved All records in set Any new record during session added to set Initial content Blank Not predetermined Data from previous entry in set Content of sub Data from Data from Data from previous sequent records previous entry initial entry record in set The Hold over and Template functions may be used simultaneously although the combined effect can be confusing making it imperative to check that records are configured properly before beginning a long ALTERDAT session in which many records are entered or modified This is particularly important when running in Interactive Mode where records are changed directly without an intervening step Command B Set audible warning when adding first record in new set Command B toggles an auditory signal that notifies the user that there is no previously entered record for the current individual Command N Create a new Linked Multiple entry Data
201. ation of the year implies a third millenium date i e 001 2001 e PEDSYS does not allow representation of year and month alone YYYYMM etc e PEDSYS does not allow two digit representation of year YYMMDD or YY alone PEDSYS programs ignore date fields that are filled with blanks or zeros event has not yet occur red or nines event has occurred but date is unknown Fa C File Types 1 Program Files The PEDSYS database system currently consists of more than 40 independently executable pro grams each designed to perform a single task Each program is stored as a single file which can be created only from compiled FORTRAN programs With the Unix operating system an executable file requires no extension Unix usage is case sensitive and by convention we use lower case for executable file names For example merge is the name of the Unix executable file containing PEDSYS program MERGE With Windows or MS DOS an executable file is named lt progname gt EXE where lt progname gt is the name of the program and EXE is an extension reserved for MS DOS executable files note that MS DOS usage is not case sensitive so that file names always appear in upper case For example MERGE EXE is the name of the MS DOS executable file containing PEDSYS program MERGE With Macintosh OS an executable file requires no extension although it is associated with the icon denoting that it is executable Macintosh OS usage is case
202. be EGO s PID whose width and Data Type match that of the EGO Permanent ID pre selected from the header input file Selection of additional items from the list permits compound sorting of data records following each header record Requests for additional information are displayed before the program is run 1 LINELIS single spaced data headers separated by blank line 2 LINEFORM thr spaces per record headers separated by blank line 3 PAGELIS single spaced data headers starting on new page 4 PAGEFORM thr spaces per record headers start on new page Select number corresponding to format of listing gt Notes e Sometimes the pre defined order implicit in PEDSYS file linkage is not desirable One way to overcome this order is to treat a linked Data File as an unlinked file which forces PEDSYS programs to ignore relationships between records defined in the Master Pointer File the Data Pointer File and the internal pointers in any Multiple entry Data File This can be accomplished 36 4 e REPORT April 19 1999 by selecting the Unlinked category in the initial File List Display and typing in the file name rather than selecting the file from the numbered list Creating a report that is based on several files can be tedious since so many choices must be made in order to control the format of each group of records If a particular report is to be run repeatedly on a production basis it is
203. bout processing history in the page heading Examples of page headings might be Example Master File SORTED Example Master File SUBSET OF reformat out SORTED SUBSET OF Blood Inventory File e Column headings are numbered and consist of one to four rows of mnemonics taken from appropriate Code File Descriptor Records e Output directed to disk file list tab is formatted as if it were to be printed except that control characters normally sent to the printer are not preserved in the file Record length of the output file is fixed at 133 characters e When LIST output is directed to the console screen record length and height of screen output is determined by the console setting in the DEVICES file Since console width is limited it is usually necessary to delete items before output can be displayed on the screen Consecutive screen pages are displayed each time a carriage return is entered from the keyboard Example Master File Top record 1 15 5 6 7 8 9 10 11 12 KID1 PSIB MSIB FSIB NKID PSIBSZ MSIBSZ FSIBSZ ID IDO61 ID056 ID038 1D042 ID066 IDO55 ID062 1D045 IDO19 ID063 1D047 ID065 ID034 IDO15 ID068 O aTr o OF WN EF MeD OO O O oO ds m O N H 12 11 11 m I NC Oo o 0 o 0o0o0oo o 5 o 05 0 ou AUO oo oo o oooo o ooo NINp_Fr_rrooooooLLO NN bsaNFEFEN ooo o ooo NINE_EHtEYtYH O oooo o 9 o 20 0 20200
204. character data See notes a and b 20 2 Set Item 20 equal to character 2 See notes a and c 19 b Set Item 19 entirely blank 19 Set Item 19 entirely blank 19 Set Item 19 entirely blank Data Type C Interpretation 7 eq 21 Is Item 7 identical to Item 21 whatever the character string 7 eq 5 6 Is Item 7 identical to Item 5 or Item 6 12 eq ID045 Is Item 12 identical to the exact string ID045 12 eq ID045 Is Item 12 identical to the exact string ID045 12 eq ID04 Does Item 12 start with the sub string ID04 12 eq D045 Does Item 12 end with the sub string D045 12 eq ID04 Does Item 12 contain the sub string ID04 in any field position 18 eq Does Item 18 contain a double quote in any field position 18 eq Does Item 18 contain an asterisk in any field position 21 eqb Is Item 21 entirely blank 21 eq Is Item 21 entirely blank 21 eq Is Item 21 entirely blank 21 eq Does Item 21 contain the character b in any field position 21 eq Does Item 21 contain a blank character in any field position gt gt gt gt gt gt gt gt gt de gt gt gt Interpretation 21 Set Item 14 equal to Item 21 whatever the character string ID015 Set Item 14 equal to string ID015 IDOLS Set Item 14 equal to string ID015 Fem Set Item 16 equal to string Fem see notes b and d ID1136 Set Item 12 equal to string ID1136 see note b b Set Item 20 entirely blank Set Item 20
205. cing a Master File requires an input file containing minimally the IDs of ID EGO FA SIRE and MO DAM These may be either Permanent or Sequential IDs In either case the sequence of numbers need not be in order and may include gaps Mnemonic codes for required entries must be used exactly as shown above for production of Master Files Choice 4 Index of any one individual without producing Master File Choice 4 automatically indexes a single individual but does not generate derived items 4 11 Pedigree Identification Numbers or Generation Numbers normally included in Master File records and a Master Pointer File is not generated A Standard Item List with no individuals pre selected for indexing is displayed when this choice is selected EGO SEQUENTIAL ID 8 SIRE S SEQ 9 DAM S SEQ 10 FIRST OFFSPRING SEQ 11 EXT PATERNAL SIB SE 12 U ER OF OFFSPRING PATERNAL SIBSHIP SIZ EGO EXT MATERNAL SIB SE 13 EX 1 SIB SEQ 14 IATERNAL SIBSHIP SIZ FULL SIBSHIP SIZE Permanent ID Birth Date YYYYMMDD Sire s Permanent ID Dam s Permanent ID Sex M F or U Exit Date YYYYMMDD Exit Code ate s Permanent ID PEDIGREE NUMBER GENERATION NUMBER INDEX FILE MASTER XMP Enter number corresponding to the individual to be indexed gt 19 Here we have chosen to add a
206. command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example tally subset out Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file tally lt n gt out may be used as input to program TALLY Output tally tab contains tabular output of the program No Code File is generated for this output file tally lt n gt out contains output of the program in PEDSYS Data File format tally lt n gt cde defines the structure of tally lt n gt out Program limits A Frequency Distribution may be tabulated for data of any type C I R or D Distribution Para meters can be computed only for numerical data types I R or D bounds on the tabulated variable may be specified only for numerical data types I R or D Number of classes may be set only for frequency distributions The number of items for which computations may be done at one time is limited to twelve for Macintosh OS and Dos Windows 50 for Unix systems Bounded distributions may be subdivided into a April 19 1999 TALLY e 44 5 maximum of 1 000 equal interval classes A maximum of 8 500 unique data values may be tabulated using Macintosh OS and Dos Windows 20 500 for Unix systems Field width of individual items is limited to 20 for Macintosh OS and Dos Windows 99 for Unix systems Fa 44 6 e TALLY April 19 1999 TRANSLAT Pro
207. consists of two records containing the name of the output file most recently produced and its associated Code File This file is produced by PEDSYS programs that produce Data Output Files with extension out The file name read from LASTFILE TMP is automatically included in the opening screen display when the user is asked to choose a file for processing SORTIN TMP Which is produced by program SORT consists of a variable number of records that a identify the information contained in the file b list the items sorted in order of significance and c give the name of the file that has most recently been processed by the SORT program This information is automatically printed on the cover page of listings produced by the program LIST Here is an example of SORTIN TMP SORTINFO Records sorted in following order major sort first June 12 1999 APPENDIX A A 21 VARIABLI VARIABLI 16 SEX SEX 12 ID ANIMAL ID 0 pedsys example MASTER XMP The 0 preceding the file name informs LIST that this is the only information about processing history that is to be printed on the cover page SUBIN TMP Produced by program SUBSET consists of a variable number of records that a identify the information contained in the file b list the criteria by which the subset was made and c give the name of the file that has most recently been processed by the SUBSET program This information is automatically printed on the co
208. contains one or more parental IDs for which individual records are not present in the pedigr fil Establish pedigree links by creating new parental records Use EGO s parental IDs but do not create new parental records Remove missing parental IDs from EGO s record r number corresponding to choice Designate paternal and maternal lineage markers Skip lineage markers When these decisions have been made COUNTPED begins execution Notes on assignment to pedigrees e COUNTPED starts pedigree assignment by locating the first founder an individual with no parents in the file and assigning this individual to Generation 0 Children of this founder are assigned to Generation 1 children s children to Generation 2 etc until all descendants have been assigned The next founder is located and the process is repeated in the same way until all descendants of all founders have been assigned Different generation numbers may be computed for the same individual as the result of descent traced from different founders In this case the larger number is assigned 12 2 e COUNTPED May 21 1999 Occasionally a data entry error may connect families in such a way that a PID appears more than once in the same pedigree When COUNTPED detects this error it terminates execution with a FATAL ERROR message and saves PIDs of all individuals for which an incorrectly entered PID including parental PIDs might account for the the error in file
209. cted the following display appears from which loci are selected for analysis 1 EGO Permanent ID 4 D1S1656 Genotypes 7 Sample No 2 Sire s Permanent ID 5 D1S515 Genotypes 3 Dam s Permanent ID 6 D2S1329 Genotypes DOWNCODE Select loci File merge out Enter number corresponding to loci for which genotypes phenotypes are to be downcoded or C to continue gt Here one locus D251329 has been chosen DOWNCODE makes two initial assumptions about gen etic loci First it assumes that data are phenotypic unless one of the last three mnemonic words associated with the Code File entry for a locus is GENO or G TYPE in which case the data are interpreted as genotypic Second the program assumes that phenotypes are autosomal codominant and follow conventions listed in Appendix C Rules for Genotype and Phenotype Nomenclature Once loci have been selected interactive or automatic mode must be selected Enter I to run DOWNCODE interactively or enter RETURN alone to run automatically gt i Here interactive mode has been selected The program begins its execution with an initial enumeration of alleles for the first locus which may take a moment if the data file is large followed by a request for the number of alleles desired after downcoding 17 2 e DOWNCODE April 19 1999 Processing D2S1329 Genotypes 6 alleles were found for D2S1329 Genotypes Enter the number of alle
210. d numbered 7 to the list of phenotypes shown in the top half of the Edit Menu 21 8 e GENOMAP June 10 1999 Locus ADA PHENO TYPE Mode of inheritance AUCD Phenotypes 1 A 2 AB If this phenotype is to remain in the table it must be associated with one or more appropriate genotypes which may entail adding allele symbols see option AA below When the DP Delete phenotype option is entered the following display appears requesting DP entry of a symbol to be deleted from the list Enter phenotype to be deleted gt D This option would return the list of phenotypes to the six shown originally above AA When the AA Add allele option is entered the following display appears requesting entry of a symbol for the new allele Enter new allele symbol gt D Here symbol D has been entered This symbol is incorporated into a series of new genotype com binations numbered 7 10 in the list of genotypes shown in the bottom half of the Edit Menu Note that the new genotypes have not been assigned to their corresponding phenotypes which must be done with the first Edit option described above DA When the DA Delete allele option is entered the following display appears requesting entry of a symbol to be deleted from the list Enter allele to be deleted gt C June 10 1999 GENOMAP e 21 9 This would reduce the list of genotypes shown in the bottom half
211. d Mnemonics File CODE STD Output countped out contains all records in the input file in their original order records contain items in the input records in the order selected followed by items a PEDNO Identification number of the pedigree of which Ego is a member b GEN Ego s generational position in the pedigree c PEDSIZ The size of the pedigree of which Ego is a member and if lineage markers have been selected d PATERNL LINES Paternal lineage markers e MATERNL LINES Maternal lineage markers countped cde defines the record structure of countped out countped err contains PIDs of individuals for which an incorrectly entered PID might account for families in which Ego appears more than once Fat 12 4 e COUNTPED May 21 1999 DATALINK Program DATALINK is a utility for linking a Single entry or Multiple entry Data File to a Master File and for establishing the internal pointers of a Multiple entry Data File Introductory Display EDSYS program DATALINK Copyright 1992 1999 SFBR DATALINK is used to link a Single entry or Multiple entry Data File to a Master File and to establish the internal pointers of a Multiple entry Data File 1 EXAMPLE MASTER FILE Enter number corresponding to a Master File to which Data Files are to be linked gt Once a Master File has been selected a Standard File List appears from which a Data File to be linked to
212. d codominant X linked dominant recessive Y linked Enter number corresponding to mode of inheritance gt This change will also be reflected in the first line of the map table for the relevant locus z Notes Any printable ASCII characters may be used for phenotype or genotype symbols except for a blank space ASCII Code 32 the open or closed parenthesis Codes 40 and 41 and the slash Code 47 Maximum length of allele symbols is 5 characters maximum genotype length is 10 characters Minimum width of genotype and phenotype fields is always twice the width of the longest char acter string representing an allele Genotypes must be represented by pairs of symbols representing both alleles There must be at least one genotype entry for each phenotype A given genotype may be mapped to only one phenotype None of the na na 1 2 autosomal genotypes or na n 3 2 X linked genotypes where na is the number of alleles may remain unmapped Many of GENOMAP s editing features frequently require that action be taken after making initial changes For example adding or deleting a phenotype symbol typically requires changes in geno type assignment and possibly deletion or addition of new genotypes Changing between X linked and autosomal mode of inheritance has significant effects because GENOMAP assigns a symbol denoting the Y chromosome to the hemizygous type in place of the second allele symbol always present in aut
213. d in the same way as the first In the example above Item 22 PSIBSZ FSIBSZ has been added to those normally found on Exam ple Master File records This was produced by entering 9 11 in the command line which specifies calculation of the ratio of PATERNAL SIBSHIP SIZE Item 9 to FULL SIBSHIP SIZE Item 11 The sequence 10 11 has also been entered in the command line which will specify calculation of the ratio of MATERNAL SIBSHIP SIZE Item 10 to FULL SIBSHIP SIZE Raising a variable to a constant power with E or e requires a leading K k before the exponent Roots are taken by raising a variable to a fractional power 5 for square root etc Examples 8EK2 9ek 1 20ek 5 etc Operators LOG and LN Preceding an item number corresponding to a numerical variable with LN In or LOG log causes its natural or base 10 logarithm to be appended to the end of each record Example the natural log of Generation number Item 20 is specified as In20 R Entering an R r produces a request for an integer seed 1 8 digits for a pseudo random number generator An item containing a randomly generated 10 digit fraction is added to the record The seed is saved in the appropriate description field of the Code File calc cde S Entering an S s adds to each record an item containing an integer 1 99999 corresponding to the record s position in the file H Entry of H h results in display of a sequence of explanatory text pages U Preceding
214. d label Tissue Box and single mnemonic BOX for a character item with a field width of 2 Entries may be replaced when the cursor is in the initial pos ition to the right of the pointer Entry of RETURN alone advances through the entries without chang ing them Entry of a space as the initial character of any field will erase the entire field Entry of as the initial character of any field results in a return to the initial Edit options screen Command A Add an Item This command produces a request for the number of an item after which a new item will be inserted April 19 1999 CODE 10 3 Command R Replace an Item Command r lt n gt results in an entry sequence that permits replacement of item lt n gt entry of r alone results in a request for an item number before entry begins Command D Delete an Item Entry of d lt n gt results in deletion of item lt n gt entry of d lt n m gt results in deletion of items lt n gt through lt m gt entry of d alone results in a request for a number or range of numbers corresponding to items to be deleted Command T Change Data File title This command makes it possible to replace the file title that is the contents of the Label Record see Appendix A Command S or X Save Code File and exit program When a Code File has been newly created entry of x or s produces the following display which gives two alternatives for saving output Enter a name for
215. d only with a system command ed in Unix Output Directory is the one to which output from PEDSYS programs will be directed Normally the output directory will be your current working directory Input Data Directory is the directory in which shared PEDSYS Master and Data files for a particu lar population reside In this example all three directories and the pathways to them are initially the same directory bdyke and path home users a Changing the Input Data Directory Note that in the display above a 3 has been entered This changes the Input Data Directory to pedsys example when the RETURN key is hit leaving the Current Working Directory and the Output Directory un changed Entry of q exits the pathway program and returns control to the Current Working Directory level E 6 INSTALLATION and SETUP Solaris 2 5 June 10 1999 b Adding Directories to DBDIRECT If you have the appropriate access permission you may add directories to the setpath directory file DBDIRECT by entering a at the prompt shown in the display above which produces the following display 1 Current 2 Other Unlisted 3 EXAMPLE Enter the pathname of the new data directory or RETURN to exit without adding a new directory gt pedsys beagles Enter the species name 1 to 11 characters or RETURN without adding a new directory gt beagles Here a new path pedsys beagles will be be added to file DBDIRECT
216. d year date d Unknown or missing dates expressed as a full field of blanks zeros or nines are skipped in age calculations No error message is generated e A data error is assumed when lower order elements day for example are present but higher order elements i e year are missing in the date This condition results in the date being skipped and an error message written to age err e Differences in length of month and leap years are taken into account e Age may be expressed in four different ways As a single item consisting of years with fraction to two decimal places As a single item consisting of months with fraction to two decimal places As a single item consisting of days without fractions As three items consisting of years months and days respectively e Ages may be negative e A blank field is generated whenever an age cannot be computed e The following sequence appears after the confirmation sequence whenever an Exit Date designated by the standard mnemonic EXIT in the Code Field is used in calculations Substitute another date for a blank EXIT date Y N gt y Enter date YYYYM ETURN alone for today s date 19981230 gt This substitution makes it possible to compute maximum ages achieved by all individuals in the population whether they are living or dead e The command line startup shortcut program name followed by a blank and an input file name may June 12 1999
217. dditions to the input Master File MASTER OLD is not produced if MASTER lt EXT gt is newly created UPDATE OLD is a backup copy of UPDATE lt EXT gt DBFILES the Directory File is written when a new Master File is created This file will be a modified version of a previously created file DPOINT lt EXT gt is created when a Master File is created setmastr log contains a record of each change that was successfully completed by the program setmastr err contains a record and diagnosis of changes that were attempted but were unsuccessfully completed because of an error or inconsistency detected by the program MPOINT lt EXT gt the Master Pointer File and DPOINT lt EXT gt the Data Pointer File are Written when the Master File is updated These will be modified versions of the previously created files Fa April 20 1999 SETMASTR 39 7 39 8 e SETMASTR April 20 1999 SHOW Program SHOW displays data items on separate lines on the screen Items from the records of EGO and both parents are displayed if the file being accessed is a Master File or a Linked Data File while a single record is displayed if the file is an Unlinked Data File Introductory Display EDSYS program SHOW Copyright 1992 SFBR HOW displays data items on separate lines on the screen 1 Unlinked File 2 sort out 3 EXAMPLE 4 LOCUS Sub directory Enter number file name or Q to quit gt 1 Displaying
218. delimited field format Any PEDSYS Master File or Data File and an associated Code File 45 12 TRANSLAT May 19 1999 Delimited fields to PEDSYS format A file containing records whose fields are separated by a unique character or sequence of characters PEDSYS to Pedigree Draw 4 4 format Any PEDSYS Master File or pedigree file and an associated Code File Pedigree Draw 4 4 to PEDSYS format Any Pedigree Draw basic pedigree file PEDSYS to FISHER MENDEL format Any PEDSYS pedigree file containing quantitative phenotypes and markers in the case of MENDEL and an associated Code File PEDSYS to S A G E REGC format Any PEDSYS pedigree file containing marker phenotypes and an associated Code File PEDSYS to CRI MAP PAP and LINKAGE formats Any PEDSYS pedigree file containing marker phenotypes and its associated Code File a Genotype Phenotype Map File Output PEDSYS to delimited field format translat tab Delimited fields to PEDSYS format translat out and translat cde PEDSYS to Pedigree Draw format translat tab Pedigree Draw to PEDSYS format translat out and translat cde PEDSYS to FISHER MENDEL format translat tab and transtab cde PEDSYS to S A G E REGC format translat out translat cde fsp par and sageregc fmt PEDSYS to CRI MAP format translat tab translt2 tab and translat err PEDSYS to PAP or LINKAGE format translat out translat cde translt2 tab and translat err PEDSYS to SOLAR MIXED format t
219. diagram below Here the four probands selected are in the last generation ancestors common to only two probands are identified by shaded symbols and ancestors common to three probands are identified by solid symbols 4 3 2 5 27 26 25 23 ID042 ID038 IDO56 IDO66 ID083 ID080 ID097 ID095 10 XE 11 28 29 24 ID063 ID062 ID047 ID103 ID109 1D111 8 13 18 17 16 15 14 9 30 31 ID045 ID034 1D077 ID070 ID054 ID068 ID015 ID019 1D113 ID124 Pi a oe Po 20 21 22 19 32 IDO71 ID049 ID069 ID067 ID130 Ei Proband Ancestor common to 2 probands E Ancestor common to 3 probands Pedigree Draw e The notion of the closest common ancestor can be seen in the pedigree diagram where neither individual ID056 nor ID066 are included as ancestors of probands ID069 and ID067 This is because any genetic contribution they make to the pedigree must be passed on in its entirety through their offspring ID047 who is designated as a common ancestor of the probands Files Input Any Master File or indexed pedigree file and Master Pointer File Input Data File or console keyboard Output ancestor tab contains a list of ancestors numbers of proband descendants and the mean April 20 1999 number of generational steps separating ancestors and probands The table in the file will be identical to the one most recently displayed on the screen ancesego out contains records for all probands ancesanc out
220. ds for offspring or missing parents there may be more records in index out than in the input file a Creating Records for Unknown and Missing Parents PEDSYS convention makes a distinction between missing and unknown parents e A missing parent is one for which no record exists in the pedigree file but whose PID appears as one of Ego s parents on one or more records in the file References to missing parents on Ego s record generate a warning message written to the index err file WARNING When the option to create records for missing parents is chosen INDEX issues a warning if a parental PID is listed as 0 integer zero This is done to help avoid problems with imported foreign pedigree data where missing parents may sometimes be designated by zeros PEDSYS designates missing data as a blank field and interprets 0 as a legitimate Permanent ID in contrast to the Sequential ID In this case if INDEX cannot find a record with Ego PID listed as 0 it will create one If more than one record contains zero PIDs for one same sexed parent the process may create unwanted half sibships e An unknown parent is one for which no record exists in the pedigree file and whose PID does not appear as FA or MO on any record in the file Unknown parents are designated by blank parental fields in PEDSYS pedigree files WARNING Creation of a record for one unknown parent requires that a record for the other known parent be present in the file
221. e Count record line 3 has been incremented accordingly F R RESELECT DIRECTORY The RESELECT DIRECTORY command appears only when one or more sub directories is present When selected the following screen display appears Select Direc la EXAMPLE 2 LOCUS Sub directory Enter number of Directory or Sub directory in which changes will be made or O to quit gt Error Messages The following error messages may appear on the screen ERROR No files named in DBFILES May 27 1999 DBFILER e 15 7 This error results in an attempt to edit or remove a file from an empty DBFILES Only ADD mode is permitted in this case ERROR MASTER lt EXT gt does not exist ERROR MASTER lt EXT gt contains no records These errors occur when attempting to add a Data File to a non existent or empty Master File respectively ERROR The extension of the Data File must be the same as th xtension of the Master File to which it is linked This error occurs when attempting to add a Data File with the wrong extension The error will not occur if the name is entered without an extension in which case the it is automatically assigned the same extension as the Master File ERROR No new Data Files with extension lt EXT gt can be added until DATALINK has been run Program DATALINK can link a single Data File to a Master File each time it is run DBFILER ref
222. e Direc tory File If DBFILES already exists the following Introductory Display appears EDSYS program DBFILER Copyright 1992 1999 SFBR Program DBFILER is used to create and modify the Directory File DBFILES making it possible to add or remove Master Files linked and or unlinked Data Files from a database Select Directory 1 Example LOCUS Sub directory Enter number of Directory or Sub directory in which changes will be made or O to quit gt 1 DBFILES OLD already exists Enter RETURN to overwrite it and continue or Q to QUIT program gt DBFILES entry new file or Sub directory to DBFILES E a file or Sub directory from DBFILES NOTE DBFILES ESELECT directory UIT program Here the Example directory choice 1 above has been selected If a sub directory is chosen choice 2 above alternate instructions in the functions display will read DBFILES entry new file to Sub directory DBFIL E a file from Sub directory DBFILI OTE Sub directory DBFILES ECT directory UIT program May 27 1999 DBFILER e 15 1 If no copy of DBFILES exists in the current directory the Introductory Display will read as follows EDSYS program DBFILER Copyright 1992 1999 SFBR Program DBFILER is used to create and modify the Directory File DBFILES
223. e Key Items The next display appears briefly before merging begins 28 4 MERGE April 19 1999 Merged records will contain the following items From MASTER XMP TARGET file 1 EGO SEQUENTIAL ID 4 EGO Permanent ID 7 Dam s Permanent ID 2 SIRE S SEQ 5 Birth Date YYYYMMDD 8 Sex M F or U 3 DAM S SEQ Sire s Permanent ID From QUANTGEN XMP DONOR file 1 ADA Phenotype 3 Tot Ser Cholestero 2 APOB Pvu2a Genotype APOAI Level Notes e Program MERGE operates by reading records of the Target file one by one and for each record searching through the Donor file for a record with a matching Key Item The searching algorithm a binary search requires that the Donor file be sorted by Key Item The program does this sort automatically e A merged record contains information from no more than one record from each of the contributing files e The number of records in MERGE OUT is always less than or equal to the number of records in the Target file e The outcome of merging linked and unlinked Single entry files is the same However differences occur in the case of Multiple entry files A linked Multiple entry Donor file will merge EGO s most recently entered record with records in the Target file whereas the particular record selected for merging from an unlinked Multiple entry Donor file is unpredictable Items selected from records in a Donor file will be repeatedly merged with each of E
224. e blank character Other delimiter may gt If choice 4 other delimiter has be 1 to 3 characters Enter number corresponding to type of separator used as item delimiter been selected the following display appears gt After any of the four choices of 45 2 e TRANSLAT Enter item delimiter enclosed in single or double quotes delimiter type the next display appears May 19 1999 Enter type of quote or if character data are enclosed in quotes Enter RETURN otherwise gt If an existing Code File is not specified the following query appears Does the first record in examped tab contain column headings Y N If the first record in the file contains column headings separated by the same delimiters as the data fields in subsequent records TRANSLAT will use these headings in constructing the PEDSYS output Code File Notes on character delimited field conversion e Normally quotes surrounding character data are needed only when commas or blanks are used as a delimiters since most software cannot distinguish between a blank or comma included as data and either character used as a delimiter e In PEDSYS to foreign translation foreign field width for any item is determined as the length of the longest string found in the corresponding field of the PEDSYS record excluding leading and trailing blanks e In foreign to PEDSYS translation TRANSLAT computes PEDSYS outp
225. e continuous traits are selected EGO Permanent ID Sire s Permanent ID Dam s Permanent ID Sex M F or U PEDIGREE NUMBER ENTIAL ID 6 ADA Phenotype ALL 7 APOB Pvu2a Genotype 12 8 Tot Ser Cholesterol 13 9 APOAI Level 10 Discrete Trait TRANSLAT Select Continuous traits RANSTEST XMP Enter numbers corresponding to items containing CONTINUOUS TRAITS to be included in output Required items have b continue to next step gt 8 Enter C to n pre selected Here Item 8 Total Serum Cholesterol has been chosen Next discrete traits are selected EGO Permanent ID Permanent ID Dam s Permanent ID Sex M F or U PEDIGREE NUMBER Sire s ENTIAL ID 6 ADA Phenotype AIT 7 APOB Pvu2a Genotype 12 8 Tot Ser Cholesterol 13 9 APOAI Level 10 Discrete Trait TRANSLAT Select Discrete Traits RANSTEST XMP Enter numbers corresponding to DISCRETE TRAITS to be included in output C to continue to the next Enter Required items have b step gt 10 May 19 1999 n pre selected TRANSLAT 45 11 Here Item 10 Discrete Trait has been chosen Finally covariates ate selected in this case Item 9 APOAI Level EGO Permanent ID 6 ADA Phenotype 11 EGO SEQUENTIAL ID Sire s Permanent ID 7 APOB Pvu2a Genotype 12 SIRE S SEQ Dam
226. e editing process are slightly different from those shown previously in that they include additional operators which make it easier to make simultaneous changes to all records belonging to a single indiv idual ALTERDAT begins its interactive data entry cycle for modification of a linked Multiple entry Data File with the following options display Updating SAMPL Interactive Mode Enter E EDIT record ADD record D DELETE record Edit control set Order of access Order is RANDOM set conFirmation display Confirmation is ON switch Log setting Log is ON set Template when adding records Fill from ID s prior record Beep if adding the first record for an individual Do NOT Beep When done with SAMPLES XMP CHANGE an existing file start a NEW file QUIT program Note that the first three commands shown E A and D are identical to those that appear when a Single entry file has been selected Command E Edit Linked Multiple entry Data File records As is the case for Single entry files entering E EDIT results in a Standard Item List from which items to be modified are selected so that only those that must be changed will appear on the Edit screen Note however that in this case the instruction lines contain an additional D operator Changes made to an item marked with the D operator on one of EGO s multiple records are duplicated automatically i
227. e field width of item 3 Subdivide item Enter number corresponding to format change required or RETURN alone to continue without changes gt In this example Pedigree Number has been selected for reformatting e Increase field width of an item Entry of 1 produces the following display Enter lt or gt plus number of LEADING or TRAILING blanks to add to field gt Field width is increased by adding blanks to the right or left margin of the item selected Example entry of lt 2 would add two blank characters to the beginning of the Pedigree Number field resulting in a new field width of seven e Decrease field width of item Entry of 2 produces the following display Enter gt or lt plus number of characters to remove from LEFT or RIGHT Enter gt MAX or lt MAX to remove from all records as many blanks as needed to remove LEADING or TRAILING blanks from the longest string in the field gt Field width may be decreased in two ways Entry of gt lt n gt or lt lt n gt simply removes characters including non blank characters from the left or right margin of the item selected Example entry of gt 2 would shorten the Pedigree Number field to three characters by removing the two left most characters Warning Data may be lost in this mode On the other hand entry of gt max or lt max removes only blank characters from the left or right margin of the field This is done
228. e out consists of a record for each individual represented in the input data file Each record contains PIDs and genotypes of EGO and each of EGO s parents downcode cde defines the record structures of downcode out downcode tab contains results of each iteration of the program and contains information on numbers of alleles and loss of information resulting from combining alleles downcode err contains records for discrepant triplets showing PIDs and genotypes of EGO and each of EGO s parents Z April 19 1999 DOWNCODE 17 7 17 8 DOWNCODE April 19 1999 DUPLIC Program DUPLIC identifies records containing duplicate entries and creates output such that each item value found a on one or more records in the input file is represented by a single record in the out put file b on two or more records in the input file is represented by the same records in the output file or c on exactly one record in the input file is represented by the same record in the output file Introductory Display EDSYS program DUPLIC Copyright 1992 1999 SFBR DUPLIC identifies records containing duplicate entries and creates output files such that an item value found a on 1 or more input records is represented by a single record in the output file b on 2 or more input records is represented by the same records in the output file or c on exactly 1 input record is represented by the same output file record Unlinked file E XAI
229. e permission of the Southwest Foundation for Biomedical Research The programs and manual may be copied and distributed to users engaged in non profit research non profit management of animal colonies or non profit health care delivery However we ask that those receiving the package from sources other than the Southwest Foundation notify us so that we may keep our distribution list current The intent of this request is to avoid problems that occur when the software and manual are out of date or incompatible We ask that users of the package report software bugs confusing instructions missing functions etc to us so that we can continue to make improvements Fa vi June 12 1999 I INTRODUCTION PEDSYS Pedigree Database System is a series of programs written for management and analysis of genealogical and demographic data The system was designed principally as a research tool for use in genetic analysis of either human or non human subjects Although some of the programs are specialized many are general enough to be used effectively with data of any sort General Principles Several criteria governed the development of PEDSYS 1 An important requirement was that PEDSYS support the collection management and analysis of data taken from the same population by investigators in several different laboratories This meant that it should be possible for anyone using the system to manage and analyze data generated in their own projects a
230. e records displayed by SHOWDATA all belong to a single individual Introductory Display EDSYS program BROWSE Copyright 1992 1999 SFBR ROWSE gives a direct display of records from a PEDSYS file a screen page at a time Unlinked File EXAI PLE LOCUS Sub directory Enter number file name or Q to quit gt If the Unlinked file category is chosen choice 1 in the example above a standard unlinked file list appears However if a directory containing linked files has been selected choice 2 in the example above an alternate Secondary File List follows This looks much like the standard Secondary File List except that it permits selection of up to five linked files for display Linked File Group for Extension XI Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels ore than one LINKED file may be selected for repeated sequential display Enter numbers corresponding to file s above in the order they are to b shown Enter RETURN alone to continue to next step In the example above the Example Master File and the Markers Quant P types file have been marked with an asterisk indicating that they have been selected for display The order of selection and display is usually not critical since switching between files is cyclical However the Master File is frequently chosen first Initial Screen Page
231. e reminding the user of the database name date of creation etc The note will not interfere with subsequent values since everything in this field is ignored d There must be a separate Master File Descriptor Record for each Master File specified in the Master File Count Record Total length is 67 characters e This field columns 1 3 contains the file extension identifying the population Entries must be left justified if less than three characters in length In the example above XMP identifies the Example population f This field columns 14 38 contains a file label that identifies the Master File for screen and print displays EXAMPLE MASTER FILE is shown in the example above g A population label is included here columns 40 50 mostly as a means of determining the appropriate terminology for screen displays and other output The name Example is shown in the example h Normally users have read only access to all PEDSYS files Four four character strings may be entered here columns 52 55 56 59 60 63 and 64 67 to serve as passwords of individuals who are given write access that is who are authorized to make changes to the Master File using program ALTMASTR i The Linked Data File Count Record specifies the total number of Linked Data Files per Master File included in the Data Directory Maximum length is 67 characters j The only field processed in this record is an integer in columns 1 3 indicating the number of
232. e to the conventions listed in Appendix C Rules for Genotype and Phenotype Nomenclature Nonetheless is it frequently helpful to generate a map for autosomal codominant loci because GENEFREQ will otherwise be forced to read through the entire Data File twice for each locus once to tally phenotypes and again to do the analysis Presence of a map file eliminates the need for the tallying step and can significantly speed execution e Calculations made from genotypes take into account the use of a dash to designate a partially known genotype for example A This situation arises when it is known that an untyped individual must have received or transmitted a particular allele allele A in the example because of the known genotypes of relatives but where inferences cannot be made about the identity of the individual s other allele shown as here In this case the known allele is counted in calculations of gene frequency while the dash is ignored e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example genefreq subset out Output Shown below are contents of output file genefreq tab and genefreq out which include computations done for ABO ADA CA1 and G6PD phenotypes and APOB Pvu2a genotype ABO and G6PD pheno types are listed in a Genotype Phenotype Map File while the remaining phenotypes are controlled by autosomal codominant loci that follow defaul
233. e to use PEDSYS effectively without extensive training Experience has shown that a common pattern for many scientists and tech nicians is to use a set of PEDSYS programs intensively for a matter of days or weeks during the course of a project after which weeks or months will pass before the system is used heavily again We therefore paid particular attention to the development of an orderly set of commands prompts and instructions that would make the programs as self instructing as possible without irritating the proficient user A major effort has been made to keep the programs consistent and easy to use We have often chosen for the sake of simplicity to write entirely new programs rather than add new functions to existing programs As far as possible we have kept the same conventions for keyboard entry and screen displays in all programs and we have paid particular attention to our use of the English language 4 PEDSYS had to accommodate constantly evolving data sets The continual changes in form and content of research data on growing animal populations required that the user be able to change or experiment with the composition and format of data quickly and without a major restructuring of the database Several features make it simple to reorganize data a The independence of PEDSYS files means that any single Data File can be created changed or deleted without affecting another Master Files provide a stable core of basic information that
234. e will be used as headers in the listing Selection of Data Files Next one or more files may be selected from which data pertaining to individuals listed in the headers is kept Select DATA Files Unlinked File EXAI PLE LOCUS Sub directory Enter number or name of file to use as DATA O gt 2 and April 19 1999 REPORT 36 1 Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Enter the number of the files s from which DATA will be taken in the order they are to be listed after the header gt 4 In the example shown here data will be taken from the Markers Quant P types file single entry and the Hemoglobin Levels file multiple entry Because REPORT does much of its formatting to conform to a particular output device the next action required is to select one of a series of output devices specified in the Printer Control File DEVICES After a file has been selected whose contents are to be listed the following display appears Output from REPORT may be sent to the following output devices Main Lab LaserWriterII Main Lab Line Printer Printer Room Sun LaserWriter Console Screen Output file list tab Enter number of device or Q to quit without printing gt Records from the files are matched by searching for the identity of Key Items that are of the same width and Data Type Program REPORT pre defines EG
235. each individual represented in the input locus data file Each record contains all the items of the input locus file in their original order with the inferred phenotype or genotype appended at the end infer2 out contains a record for each individual in the Master File or pedigree file for which an original phenotype is available or for which a phenotype or genotype can be inferred infererr out I lt locusfilename gt cde infer2 cde infererr cde Recursive use of output files is permitted that is file inferl out or infer2 out may be used as input to program INFER Algorithm R H King L Freeman Shade April 20 1999 INFER e 23 13 23 14 INFER April 20 1999 ITEMIZE ITEMIZE is a program used a to determine the PEDSYS format of records in files imported from for eign database systems b to modify this format and c to create a PEDSYS Code File and or a Data File from the original data The program shares some features of programs CODE and REFORMAT but does not replace them Initial Display EDSYS program ITE E Copyright 1992 1999 SFBR EMIZE determines the PEDSYS format of foreign ASCII data records Enter the name of the file for which PEDSYS format is to be defined gt MASTER XMP Enter the name of the Code File for MASTER P or enter RETURN to create a new Code File gt When the name of the input data file and the s
236. ecord 2 2 Page 1 1 EDIT Mode Random Order Sample ID Number gt 5582 lt Sample Type gt R lt Date Taken gt 820811 lt Vial Type gt TYG lt Sample Status gt lt Animal Status gt lt Diet Project gt H lt Comment gt AB 2 3 4 5 6 7 8 9 Enter R to R E or A to APPEND to Comment Sr Enter item one or more spaces will blank item Comment gt lt April 20 1999 ALTERDAT e 4 13 The R command simply replaces any existing comment with a new entry The A command on the other hand makes it possible to append information to a previously entered comment The item may have any label although common ones are Comment Notes etc The Comment entry will be truncated if it extends beyond the item field width boundary If this feature is unwanted the reserved mnemonic should be avoided for example NOTES or COMM etc might be substituted e When running in Batch Mode ALTERDAT saves changes and additions in file lt filename gt UPD which is used in turn as input to program SETDATA Because deletion of records may require adjustments of the pointers upon which the PEDSYS file structure depends IDs of records to be deleted are saved by ALTERDAT in file lt filename gt DEL which is used in turn as input to program DELRECS the same program used to delete records from Master Files DELRECS must be run after records have been selected for deletion in either Batch o
237. ecords contain minimally IDs for Ego and Ego s parents These conditions are fulfilled automatically if a Master File is selected but an unlinked Data File requires preprocessing with program INDEX Fa Calculating inbreeding coefficients Inbreeding coefficients are calculated for individuals when choice 1 or 3 is selected in the command line of the Introductory Display Once a Master File or indexed pedigree file with an appropriate Master Pointer File has been selected the following display appears from which the source of probands for which inbreeding coefficients are to be calculated may be chosen April 20 1999 KINSHIP 25 1 Coefficients may be calculated for individuals entered from 1 Keyboard 2 Unlinked File 3 EXAMPLE 4 LOCUS Sub directory Enter number above corresponding to the appropriate source of probands gt 1 1 Proband IDs entered from the keyboard Choice 1 shown above specifies that Ego IDs are to be entered one by one from the keyboard Enter P if individuals are identified by Permanent IDs or S if by Sequential IDs gt Enter Ego Permanent ID RETURN alone terminates entry gt ID034 lt ID gt ID015 lt ID gt lt ID Save all output records in file kinship out Discard output records with zero coefficients Save records with non zero coefficients in kinship out zero coefficients in nokinship out Enter number corresponding
238. ed for comparison so that records are grouped together but other items such as dates may be added as minor sorts so as to order records within groupings e The first record in each of the groupings is the one selected for inclusion in the Keep single records Choice 1 category above e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example duplic subset out Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file duplic out or noduplic out may be used as input to program DUPLIC Output duplic out contains records from the input file in which selected entries have been found noduplic out contains records from the input file that are excluded from duplic out duplic cde and noduplic cde define the record structure of duplic out and noduplic out respectively a April 20 1999 DUPLIC 18 3 18 4 e DUPLIC April 20 1999 FOUNDREP Program FOUNDREP determines the extent to which population founders individuals with both parents unknown are represented in members of the current living population Introductory Display EDSYS program FOUNDREP Copyright 1999 SFBR FOUNDREP determines th xtent to which population founders individuals with both parents unknown are represented in members of the current living population PORTANT The file from
239. een selected whose contents are to be listed the following display appears Output from LIST may be sent to the following output devices Main Lab LaserWriterII Main Lab Line Printer Printer Room Sun LaserWriter Console Screen Output file list tab Enter number of device or Q to quit without printing gt Next items to be listed are selected EGO SEQUENTIAL ID ER OF OFFSPRING 15 Dam s Permanent ID SIRE S S ERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ L SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB S EGO Permanent ID 19 Mate s Permanent ID EXT MATERNAL SIB SI Birth Date YYYYMMDD 20 PEDIGREE NUMBER EX L SLB SEQ Sire s Permanent ID 21 GENERATION NUI LIST Items to be listed File MASTER XMP Enter numbers corresponding to items shown above in the order they are to appear across the page Precede the number with gt or lt for RIGHT or LI justification Enter A to list all items B to insert blanks C to continue to next step gt April 20 1999 LIST 26 1 Commands Item number Selection of items within records is accomplished by entering lt n gt the number corres ponding to the item in the list above the instruction line in the order that items are to appear
240. een chosen Notes on CRI MAP conversion e CRI MAP requires that IDs of Ego and Ego s parents be in integer format e TRANSLAT converts genotype representation from PEDSYS to CRI MAP format where for each locus allele symbols are replaced by integer values corresponding to their alphabetic order and geno 45 8 TRANSLAT May 19 1999 types are converted to numerical form Missing allele symbols are represented by zeros in CRI MAP format See Appendix B Program TRANSLAT Format Translations for more detail on CRI MAP record and genotype format e When TRANSLAT finds a phenotype in the PEDSYS input file for which alleles have not been assigned the phenotype symbol on Ego s record is changed to zeros and an error message is written to file translat err The format of error messages is Locus lt locus name gt Record lt recno gt Uninterpretable lt entry gt where lt recno gt identifies the position of the record in the input file and lt entry gt is the symbol that caused the error 9 PEDSYS to PAP genotypes TRANSLAT converts PEDSYS genotype coding to PAP Hasstedt 1989 format Records of output file translat out contain EGO PID original genotype phenotypes and converted genotype symbols Other information parental IDs sex family number etc is not included EGO Permanent ID 6 ADA Phenotype EGO SEQUENTIAL ID Sire s Permanent ID 7 APOB Pvu2a Genotype SIRE S SEQ Dam s Permanent ID 8 Tot Ser Chol
241. efore modification are aved with extension OLD and DELETE lt EXT gt is renamed DELETE OLD DELRECS updates a Data File from changes stored in lt datafile gt DEL Data File records are deleted and the file as it was before modification is saved in lt datafile gt OLD lt datafile gt DEL is renamed lt datafile gt ODE DPOINT lt EXT gt is regenerated when deletions occur in a Linked Data File Unlinked file EXAMPLE LOCUS Sub directory Enter number file name or Q to quit gt Error Messages and Displays Program DELRECS is usually run as a last step in permanently updating Master Files or Data Files Because its output plays such a critical part in the organization of pedigree databases considerable effort has gone into preventing errors from being incorporated into the data Protection from permanent damage is provided at three levels a Errors that affect single records are recorded in the delrecs err file and the record in question is not deleted b Whenever possible the program is stopped before the final creation of new files when errors are found that might affect file structure c Backup copies of original input files are created so that it is always possible to discard i ncorrect changes and return to an earlier version of the data se Linked Files There must be a record in the Master File for every PID to be deleted from a
242. elect quantitative data Enter numbers corresponding to QUANTITATIVE data items to be included in output decimal points will be added to integer values as needed Required items have been pre selected Enter C to continue gt 8 9 Items 1 through 5 are pre selected and are protected from further change Items 8 and 9 represent variables that may be selected for inclusion in the output file Program MENDEL requires genetic marker loci chosen in its initial Item Selection Display EGO Permanent ID 6 ADA Phenotype ENTIAL ID Sire s Permanent ID 7 APOB Pvu2a Genotype Dam s Permanent ID 8 Tot Ser Cholesterol Sex M F or U 9 APOAI Level PEDIGREE NUMBER 10 Discrete Trait TRANSLAT Select marker locus RANSTEST XMP Enter numbers corresponding to items containing genotypes or phenotypes to be included in output Required items have been pre selected Enter B to insert blanks C to continue to next step gt 6 7 45 6 TRANSLAT May 19 1999 Here again items 1 5 are preselected while items 6 and 7 represent a loci that may be selected for output Also provided is an opportunity to insert blank fields into the record which can be filled in at a later time When selection of markers is complete quantitative variables are chosen from a display identical to that shown for FISHER above When all data have been chosen the followin
243. em 8 in the display above are as follows S indicates that the father s genotype is inconsistent with the genotypes of Ego and Ego s mother D indicates that the mother s genotype is inconsistent with the genotypes of Ego and Ego s father SorD indicates that a discrepancy exists but that it is not possible to determine which is the discrepant parent SandD indicates that both the father s and mother s genotypes are inconsistent with Ego s genotype FMLY indicates that discrepancies are found when grandparents and entire sibships are considered even though single EGO FA MO triplets are consistent with Mendelian laws z Notes e Enclosure of a discrepancy code in parentheses for example Sor D or M indicates that the parental genotype has been inferred from genotypes of other family members e INFER automatically substitutes the symbols S for sire and D for dam in nonhuman animal populations F for father and M for mother in human populations e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example infer subset out 23 12 INFER April 20 1999 Files 1 Single files containing genotypes or phenotypes for one or more loci Input Output A Master File and a Data File having records containing genotypic or phenotypic data with associated Code Files The Data File need not be linked if it contains pedigree data or if the pedig
244. en an input Code File is used the original item descriptor labels remain unchanged even when a new mnemonic is entered c The item descriptor label remains unchanged when a missing Standard Mnemonic is added To bypass these limitations use program CODE to modify file itemize cde Notes e To reduce file storage requirements some computers and programs ignore trailing blank characters at the end of records Because most PEDSYS programs require that all Data Records be exactly the same length it is safer to allow ITEMIZE to write itemize out in which trailing blanks are always included even when inclusion of skipped fields means that it is simply a copy of the input Data File Files Input Any formatted ASCII text file with or without a Code File Output itemize out contains a copy of the input file with or without the inclusion of fields designated to be skipped itemize cde defines the structure of itemize out Program Limits A maximum of 500 items may be defined for any one PEDSYS record Width of a record displayed on the screen may not exceed 1024 characters April 20 1999 ITEMIZE e 24 9 24 10 e ITEMIZE April 20 1999 KINSHIP Program KINSHIP calculates coefficients of kinship 6 for pairs of individuals or inbreeding coefficients F by either the Stevens Boyce or the Quaas Henderson algorithm Boyce 1983 The file from which pedigrees are read may be either a Master File or an indexed pedigree file c
245. ent When entry for the first segment is completed the following display appears Subdivide Birth Date YYYYM Segment 2 gt 2 lt Enter number of characters 1 4 to be assigned to this segment The process is the same as that used in program ITEMIZE the number and mnemonic of the newly created segment is displayed above underline characters _ that form a segment ruler The Item Ruler is reduced in size correspondingly and the next segment number is displayed above a new command line This pattern is followed until subdivisions of the original item are completely defined The number of subdivisions must be no greater than the original field width of the item selected April 19 1999 REFORMAT 35 3 J Two or more items may be joined together with this command which produces the following display EGO SEQUENTIAL ID ER OF OFFSPRING 15 Dam s Permanent ID SIRE S S ERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB SI EGO Permanent ID 19 Mate s Permanent ID EXT MATERNAL SIB SI Birth Date YYYYMMDD 20 PEDIGREE NUMBE EXT FULL SIB SEQ Sire s Permanent ID 21 GENERATION NU RMAT tems to be joined File MASTER XMP Enter numbers corresponding to
246. ent ID EDIGRE E NUMBER ENERAT Kids Si ION NU bs Ratio Items to be converted MASTER XMP AND O R 1 gt gt gt gt k gt Last entry EN ELS step IF gt 16 eq M THEN gt 18 k3 H for explanation 1 lt gt k0 8 1 8 IF 161 1 shortcuts Enter lt Item No gt lt Operator gt lt Test gt Enter lt Ttem No gt lt Change gt may be compound AND gt 8 lt 9 10 11 THEN gt 22 8 11 OR gt IF gt 21 ne 13 75 examples RETURN alone to continue Shown here is an example of a change to a compound value that is dependent on values of other items on the record Item 22 Kids Sibs Ratio is a new item added prior to starting the table The value of this item is dependent on the values of Item 8 NUMBER OF OFFSPRING and Item 11 FULL SIBSHIP SIZE If Item 11 is non zero Item 22 is set to the value of Item 8 divided by the value of Item 11 Otherwise Item 22 is set to the undivided value of Item 8 When all items have been chosen for conversion the following display appears showing entries in the Conversion Table and providing an opportunity to edit them IF EX IF EX IE IF NKI EX FSIBSZ D KO TH EN SEX 2 EN SEX 1 EN SEX 3 EN KidSib
247. ental information may be used with or without creation of new parental records if it is ignored both Sequential IDs and Permanent IDs are removed from Ego s record The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example countped subset out If the input Code File file contains mnemonics PEDNO GEN and PEDSIZ COUNTPED preserves these items renames them OLD PEDNO OLD GEN and OLD PEDSIZ respectively and appends newly computed items at the end of each record This is in contrast to program INDEX where the original items are replaced May 21 1999 COUNTPED e 12 3 Note on lineage marking e COUNTPED starts lineage marking by assigning an arbitrary integer code to each founder Then beginning with individuals of either sex in the most recent generation maternal and paternal lineages are determined by tracing links upward through ancestors of the same sex until a founder of the same sex is reached All descendents in this line are assigned the integer code of the female founder as a maternal lineage marker and the code of the male founder as a paternal lineage marker The file may then be sorted on markers to isolate and identify paths of maternal or paternal genetic transmission Files Input 1 Any Master File or pedigree file having records containing a unique identifier for an individual and his or her parents and an associated Code File 2 The Standar
248. enter C to continue gt In the example above EGO Permanent ID Sample ID Number and Project Items 1 2 and 7 have been allocated to locked columns using common spreadsheet terminology at the left most side of the display The remaining items remain unlocked ES XMP ID ID097 Items 9 Recs 3 LIFO Page 1 1 FilePos 1 96 1 2 7 3 sde 6 8 9 ID SAMPLE PROJ DATI VIAL SAMPLE ANIMAL COMMNT PNTR TAKEN STATUS STATUS an an ID097 W219 HIM 1988 12 22 TYG 2 ID097 S219 HL 1980 07 01 9ML LOW HOSP 1 ID097 R219 HL 1980 07 01 2ML CRIT HOSP 0 Enter lt n gt or lt n gt for new page PID S lt n gt 1 32 or lt n gt 1 96 to set top row gt or lt lt n gt to shift window I lt n gt 1 9 to set window L to lock columns O to change order to switch files N for new file H for help Q to quit gt 41 6 SHOWDATA April 19 1999 Items in locked columns form a subset of other items displayed and are positioned in order of selection from the left most boundary of the screen They remain visible in their locked positions despite subsequent horizontal shifts of the remaining items selected for display Locking is particularly useful for maintaining visibility of a PID while shifting horizontally across long records Any item not explicitly designated as locked is assigned by default to the unlocked display Items in the unlocked portion are positioned in order from the
249. entirely blank Set Item 20 entirely blank a Warning Data type change applies to all entries for this item b Warning Field width of item will be increased c Warning All entries for this item will be left justified d Leading and trailing blanks honored April 19 1999 NEWITEM 29 7 e A dummy value SKIP is sometimes helpful in constructing compound sequences For example if 16 eq M or 16 eq U then skip else 16 Fem would change the female Sex Code from F to Fem leaving males and unknown sex codes in their original form e NEWITEM performs its tests in order and makes no permanent changes until all tests have been completed for each input data record This means that a command sequence entered at the top of the list in the Conversion Table may be overridden by a sequence entered later in the list For example the following pair of command sequences if 16 eq M then 16 k1 if 16 eq F then 16 k2 else 16 k3 fails to change SEX code M to numeral 1 as specified in the first line because it is superseded by the second sequence The following command set will change all codes if 16 eq M then 16 k1 if 16 eq F then 16 k2 if 16 eq U then 16 k3 The sequence of operations also means that new items created in the current NEWITEM run are initially blank and thus will not contain useful test values until the program has finished its execution e A
250. ep gt In the example above the Markers Quantitative Phenotypes and the Hemoglobin Levels files have been marked with an asterisk indicating that information will be extracted from both files Case 2 Triplet data extracted from a single Unlinked File If an unlinked Data File is chosen that includes pedigree information that is if its Code File contains standard mnemonics EGO ID SIRE FA and DAM MO the following query appears June 5 1999 TRIPLETS 46 1 Unlinked Fil EXAMPED XMI PEDTRTES TRANSTEST WEIGHTS XMP XI XI Enter a file number or name gt 1 Use pedigree information found in E gt y Here file EXAMPED XMP has been selected This file contains full pedigree information which will be used in constructing triplets If however a file is chosen for which the Code File does not con tain the standard mnemonics the following instruction appears Pedigree information is not present in file WEIGHTS XMP 1 Unlinked File 2 Example Master File Enter number of file containing pedigree information gt 2 In the example above IDs of Ego and Ego s parents were not found in file WEIGHTS XMP from which triplet data are to be extracted The Example Master File choice 2 has been selected to supply pedigree information When a pedigree file has been chosen an Item List Display of the first Data Fi
251. equence followed by RETURN shifts the unlocked portion of the window horizontally by lt i gt items without changing page position In the example above 1 lt lt i gt lt 4 since there are 4 items per record in the Hemoglobin Levels file I lt i gt where lt i gt is an integer in the range 1 through lt nitems gt the number of items on the record Entry of this sequence sets the horizontal position of the item selected at the left most unlocked column When RETURN is hit the same page is displayed with the window shifted horizontally as specified In the example above 1 lt lt i gt lt 4 since there are 4 items per record in the Hemoglobin Levels file L Entry of this command makes it possible to lock columns that is fix their position so that they remain visible despite horizontal shifts of the display window see explanation below P The page command is used when more than one display page is required for an individual s multiple records Entry of p displays the next page p lt n gt the lt n gt th page O The default order in which records of a Multiple entry Data File are displayed is LIFO last in first out with the most recently entered records appearing at the top of the screen The O command switches back and forth between LIFO and FIFO first in first out with the most recently entered records displayed at the bottom of the list N This command results in a return to the File List from which a new file or set of fil
252. er only when mnemonic words specified in the table are identical to those in the Code File accompanying file to be modified If a mnemonic occurs in the table that matches none in the Code File the following message appears and the program terminates ERROR Table mnemonic does not match Code File mnemonic Input 1 Any Master File or Data File and an associated Code File 2 A Conversion Table File as defined above Files Recursive use of output files is permitted that is file newitem out may be used as input to program NEWITEM Output newitem out contains all records of the input file in the order they have been selected with specified items changed according to the Conversion Table newitem cde defines the record structure of newitem out Items are ordered according to the sequence in which they are selected newitem tab contains a new or revised Conversion Table This file is created each time a new Conversion Table is generated or when a previously created Table is edited Program limits 100 Conversion table entries 20 test or change values within square brackets z April 19 1999 NEWITEM 29 9 29 10 NEWITEM April 19 1999 PEDTRIM PEDTRIM simplifies a pedigree by removing individuals that contribute no information to genetic analysis The program iteratively removes from a pedigree all individuals whose phenotypic or genotypic data are missing or known to be of poor quality if they have a no
253. er than 126 The following errors may be reported if any of these values is found lt ego gt Record not added unprintable character ASCII lt nasc gt found 01 lt ego gt lt mne gt not changed contains unprintable character ASCII lt nasc gt 02 where lt ego gt is the PID of the record to be updated in lt filename gt UPD lt nasc gt is the ASCII code corresponding to the unprintable character in the lt filename gt UPD record and lt mne gt is a mnemonic identifying the item in file lt filename gt UPD Error 01 may occur when adding a new individual Error 02 when making changes to a record already in the Data File Probable causes of these errors are a an incorrect key combination hit during data entry b disk error or c a noisy communication line during data transfer To correct Error 01 re enter entire record using ALTERDAT in ADD mode To correct Error 02 re enter item using ALTERDAT in EDIT mode Re run SETDATA using the most recent Update and Data Files see note on renaming and deleting these files Group 1 Mismatched Mnemonics A check is done to assure that mnemonics identifying items in lt filename gt UPD correspond to those in the Code File associated with the Data File The following error is reported if the update mnemonics do not match the mnemonic fields in the appropriate Descriptor Record of lt filename gt CDE lt ego gt Entry not changed lt mnel gt lt mne2 gt lt mne3
254. erson method starts at the top of a pedigree and computes kinships for individuals in subsequent generations on the basis of coefficients already computed This approach avoids repeated counting of complete loops but requires computations even for unrelated parents Thus Stevens Boyce is usually more efficient for calculations of coefficients in pedigrees where average kinship is low while Quaas Henderson is better for large deep pedigrees of higher average kinship The table below gives comparisons of the two methods used to calculate inbreeding coefficients for individuals in four separate populations from Southwest Foundation for Biomedical Research pedigree databases Both methods yield exactly the same numerical results April 20 1999 KINSHIP 25 7 Population Monodelphis domestica Baboons Humans 1 Humans 2 Colony Size 30 162 50 11 450 6 462 21 857 No of Pedigrees Max Gen erations 22 22 41 46 F 2781 2293 0046 0000 0344 Stevens Boyce 6 35 48 0 1033 003418 0 24 53 Quaas Henderson 225 2005 313 206 236 32 14 42 05 14 Gray short tailed opossum Random sample of 50 drawn from colony e The inbreeding coefficient of an individual is identical to the kinship coefficient measured between that individual s parents e The coefficient of kinship calculated for an individual that is for self is 1 0 e It is sometime
255. es may be selected for display in the usual manner H Entry of an H produces the following help display pages To display records belonging to a specific individual enter EGO s PID or S followed by EGO Sequential ID as it appears in the Master File To display records without reference to IDs enter followed by a number representing position of a record in the file Entry of lt n gt or lt n gt moves through the file displaying records belong ing to a series of individuals whose order depends on the sequence of records in the Data File NOTE Use of this command with Linked Files may result in an unpredictable sequence of individuals displayed To shift the window RIGHT or LEFT enter gt or lt for shifts of one item gt lt i gt or lt lt i gt respectively for shifts of lt i gt items To set the item that will appear in the left most unlocked column enter I lt i gt where lt i gt is the item number then hit return Enter C to return to data display Enter P to page gt 41 4 SHOWDATA April 19 1999 and Enter L to select columns for LOCKED display that is fixed in position on the left hand side of the screen despite horizontal movement of the dis play window Enter O to switch between LIFO and FIFO order of multiple records records they may be chosen Enter N to select new files for display Enter Q t
256. es and extensions of all files are consistent ERROR DPOINT lt EXT gt does not exist DATALINK creates a Data Pointer File if it does not already exist when only one Data File is listed in DBFILES This error message occurs when DPOINT lt EXT gt does not exist but more than one Data File is listed in the Directory File To correct this error begin the file linking process from the start remove all Linked Data File Descriptor Records from DBFILES using program DBFILER Then April 20 1999 DATALINK 13 1 also with DBFILER add a single Data File to DBFILES and run program DATALINK Repeat the DBFILER DATALINK sequence until all files have been linked ERROR Number of Data Files listed in DBFILES does not correspond to the number of pointer fields in DPOINT lt EXT gt The safest way to recover from this error is to begin the file linking process from the start delete file DPOINT lt EXT gt and remove all Linked Data File Descriptor Records from DBFILES using program DBFILER Then also with DBFILER add a single Data File to DBFILES and run program DATALINK Repeat the DBFILER DATALINK sequence until all files have been linked ERROR Permanent Ids in Master File and Data File not the same field width To correct this error change PID field width in the Data File using program REFORMAT Notes e Only one Data File may be linked at a time DATALINK must be run each time a Data File is added to the Directo
257. es when errors are found that might affect file structure Level 3 Backup copies of original input files are created so that it is always possible to discard incorrect changes and return to an earlier version of the data Here are the error messages that may appear in file setmastr err and the measures that should be taken to correct them For convenience errors are grouped into seven classes Group 0 Unprintable characters In order to prevent unprintable characters from being added to the Master File records each new entry in UPDATE lt EXT gt is scanned for characters with ASCII decimal code values less than 32 or greater than 126 The following errors may reported if any of these values is found lt ego gt Record not added unprintable character ASCII lt nasc gt found 01 lt ego gt lt mnel gt lt mne2 gt lt mne3 gt lt mne4 gt not changed contains unprintable character ASCII lt nasc gt 02 where lt nasc gt is the ASCII code corresponding to the unprintable character and lt mne1 gt etc are mnemonics identifying the item in the UPDATE lt EXT gt record Error 01 may occur when adding a new individual Error 02 when making changes to a record already in the Master File Probable causes of error are a incorrect key combination hit during data entry b disk error or c noisy communication line during data transfer To correct Error 01 re enter entire record using ALTMASTR in ADD mode To correct Erro
258. esponding to identifiers by which input record sets will be defined prior to extracting data items typically an Ego ID Enter C to continue gt Next the option to sort records within sets is selected EGO SEQUENTIAL ID ER OF OFFSPRING 15 Dam s Permanent ID SIRE S SEQ ERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SI ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB S EGO Permanent ID DO s Permanent ID EXT MATERNAL SIB SI 13 Birth Date YYYYMMDD 20 PEDIGREE NUMBER EX 1 SIB SEQ 14 Sire s Permanent ID 21 GENERATION NUMBER COMBINI Sort within groups File MASTER XMP Record sets will be defined as marked above Optionally enter one or more numbers corresponding to items by which records will be sorted within sets precede with D for descending order Enter C to continue to next step gt Here input records will be sorted by Birth Date Item 13 so that sibship data will be ordered like wise on the output record Step 2 Selecting Items to Include on Combined Output Records is next EGO SEQUENTIAL ID 8 ER OF OFFSPRING 15 Dam s Permanent ID SIRE S S 9 ERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE 10 ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exit
259. ess of the month or day included in the date e The substring feature also permits the use of compound coding To illustrate this technique at the Southwest Foundation many animals are used as subjects in more than one research project Rather than add a separate item for each project code to records in the Master File we have combined codes into a single item In our scheme H signifies that the animal is used in a heart disease project and P indicates that the individual is included in a panel of animals used to characterize various genetic marker systems Several code combinations are possible H_ P_ HP PH and __ Constructing a subset by including records having the substring H anywhere in this item will assemble a file containing all animals in the heart disease project regardless of their panel membership excluding records containing the substring _ would result in a file containing all animals used in both projects etc e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example subset sort out Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file subset out or nosubset out may be used as input to program SUBSET Output subset out contains records that meet criteria for inclusion in the subset in the same order as in the input file nosubset out contains a complementar
260. esterol DAM S SEQ Sex M F or U 9 APOAI Level PEDIGREE NUMBER 10 Discrete Trait TRANSLAT Select locus TRANSTEST XMP Enter numbers corresponding to loci for which genotypes phenotypes symbols are to be converted to PAP form Required items have been pre selected Enter C to continue gt EGO Permanent ID Item 1 is preselected and protected from further change Here ADA Pheno type Item 6 and APOB Pvu2a Genotype Item 7 have been selected Note on PAP conversion e PAP genotypes are represented as integers whose value is determined by genotypic array position See Appendix B Program TRANSLAT Format Translations for more information on PAP genotype formats 10 PEDSYS to LINKAGE format Translation to LINKAGE format produces a PEDSYS file formatted correctly for input to the LINKAGE preprocessing routine MAKEPED not to be confused with the PEDSYS program with the same name Assignment of SEX and IDs of EGO FA and MO fields is required if standard mnemonics for these items are not found in the input file Otherwise the first step in this conversion is to select the item representing EGO s affection status that is whether EGO is designated as an individual affected with a disease or other phenotype of interest May 19 1999 TRANSLAT 45 9 EGO Permanent ID 6 ADA Phenotype ENTIAL ID Sire s Permanent ID 7 APOB Pvu2a Genotype Dam s Permanen
261. et has been entered in the initial position of any field either a the new values will be redisplayed for confirmation or b a request for another ID is given depending on the Confirmation setting see below An example of a Sequential Edit display follows ID ID069 EDIT Mode Seq Order Enter items below as prompted one or more spaces to blank an item RETURN for next item or for next step ADA Phenotype gt B lt APOB Pvu2a Genotype gt i Tot Ser Cholestero1 gt 103 lt APOAI Level gt 99 2 lt Here the cursor is positioned at the first character of the first item ADA Phenotype selected for modification Entry of any printable character except will replace the current contents of the item here B entry of RETURN moves the cursor to the next item entry of or replacement of the last item moves the cursor to the command line at which point entry of S saves the record entry of E switches the program to Random Order for purposes of editing or entry of X results in a request for another record to edit Command F Set confirmation status Sequential Order only Entry of an F at the command line toggles an ON OFF setting of the confirmation display With the order of entry set to Sequential and Confirmation ON the default a newly edited or added record is redisplayed for inspection and the opportunity is provided to make additional changes save the entries as they appear or to qui
262. explicitly designated as locked is assigned by default to the unlocked display Items in the unlocked portion are positioned in order from the right most locked column Visibility of 8 4 BROWSE April 19 1999 items in the unlocked portion depends on their number the width of the unlocked segment of the window and the position of the window as specified by the relevant command sequence The Find function se The total formatted width of locked items may not exceed width of the screen Columns may be unlocked that is returned to their original order by entering LO The Find function can be activated in one of two ways Entering F alone at the command line results in a Standard Item List with a request for the value sought for the particular item in EGO s record When this has been entered instructions for starting the search are given EGO SE Q U ENTIAL ID SIRE S SE Q DAM S SI EO FIRST OFFSPRING SEQ EXT PA ERNAL SIB SE 8 9 PA 10 11 12 U 15 16 17 18 19 ER OF OFFSPRING ERNAL SIBSHIP SIZ IATERNAL SIBSHIP SIZ FULL SIBSHIP SIZE EGO Permanent ID EXT MA ERNAL SIB SE EXT FU L 1 SIB SEQ quot gt 8 eq current record gt es 2 Enter item number 1 13 14 relational Enter record number at which to start search 20 21 Birth Date YYYYMM
263. f Sequential IDs appearing as an item immediately following the PID of the individual selected for indexing z Assignment of Pedigree ID and Generation Numbers INDEX identifies genealogical links in a pedigree file and assigns numbers to each individual corresponding to the pedigree to which he or she belongs as well as the generational position of that individual in the pedigree Singletons may be assigned either to Pedigree Number 0 or to their own in dividual pedigree Founders are assigned to Generation 0 with numbers increasing through more recent generations This function is automatic except for Choices 3 and 4 where no assignment of these variables is done INDEX maintains the record position of items containing Pedigree ID and Generation Numbers if mnemonics PEDNO and GEN are found in the input Code File Otherwise the newly derived variables are placed at the end of the output record April 19 1999 INDEX e 22 7 Order of Records in the Output File INDEX automatically sorts output records in the following order Pedigree ID Number Generation Number Father Sire Mother Dam Birth Date if present and EGO PID This groups members of the same pedigree in adjacent positions and maintains the correct parent offspring order parents always precede their offspring As a consequence of this sorting sequence records in index out may not be in the same order as those in the input file Also if the option is chosen to create recor
264. f the program is to extract items from record sets in a Multiple entry file where sets are defined by Ego PID and place these items in some order on a single output record also identified by Ego PID The program is also used with Single entry files where record sets are defined by some identifier occurring on more than one record such as a parental PID Introductory Display EDSYS program COMBINE Copyright 1992 1999 SFB COMBINE produces single new records each containing one or more values ex tracted in sequence from a Data File containing SETS of records defined by a common identifier for example the same Ego ID or same parents etc Unlinked file EXAMPLE LOCUS Sub directory Enter number file name or Q to quit gt 2 In this initial example we select the Hemoglobin Levels File a Multiple entry Data File and proceed through the steps that will combine hemoglobin measures for each individual on one record Step 1 Selecting Key Items by which Input Records Are Sorted into Sets Once a file has been selected the screen shown below is displayed from which one or more key items defining record sets are chosen 1 Ego 3 Hemoglobin Level 2 Sample Date 4 INTERNAL POINTER COMBINE Select Identifiers File HEMOGLOB XMP Enter one or more numbers corresponding to identifiers by which input record sets will be defined prior to extractin
265. f the data display The item number 1 appears first with mnemonic SEQ just below it Below this is a row of five underline characters _ forming an Item Ruler This pattern is repeated for subsequent assignments using command A with new items appended to the new row left to right while the row of unassigned characters recedes correspondingly With each new item defined the Input Ruler is repositioned so that its leading character is located at the start of the unassigned portion of the input record The next display shows the result of having defined two additional items and the start of designating the next as a skip field 042011D042 Item 4 ER XMP Record 1 of 32 Length 95 Lele epee eee sy ens O 01D06119720309 gt 32 lt Enter number of characters to be assigned to this item 1 80 gt S lt Enter the Data Type of the item C I or R or S to skip Here the next 32 characters of the input record starting at the blank character four spaces prior to the 7 and ending with the 0 just before the characters ID061 will be assigned to a single item with the mnemonic SKIP The result of this operation are shown below 804201ID042 Enter A to S to M to W to X to 24 4 e ITEMIZE ER XMP Record 1 of 32 ASSIGN next item SUBDIVID change M E Item EMONIC change WIDTH of Item SAVE and EXIT Length 95 re srseslseta 0 ID061
266. file directory see Chapter II SETUP and INSTALLATION Information about the files that PEDSYS programs are to process is provided in a file that is associated with such a directory This file contains the name of one or more Master Files the numbers and names of linked Data Files access privileges and variables that control the way in which program ALTERDAT displays data to be edited Directory Files may be created with the PEDSYS program DBFILER or with any ASCII editor The Directory File for any directory must be named DBFILES An example of a Directory File for the Example database is shown below Master Files Example Master File Linked Data Files QUANTGEN Markers Quant P types SAMPLES Blood Sample Inventory Gi UW U U EMOGLOB Hemoglobin Levels H Unlinked Data Files PED XI D RTEST X STEST X HTS XMP Sub directories 1999 02 15 S EJ AZES ti H Q E O Quik a Records in this file are formatted as follows Record 1 Master File Count Record a Key b c Map e e e 00000000000000000000900000000000000000000000000000000000000000000 Start 1 4 Format I3 Record 2 Master File Descriptor Record s d A 12 e APPENDIX A June 12 1999 Key e Map 0000000000 Start 1 14 Format A3 10X A25 1X A11 1X 4A4 Record 3 Linked Data
267. file reformat out may be used as input to program REFORMAT Output reformat out contains all records in the input file in the order selected reformat cde defines the record structure of reformat out Program Limits A maximum of 500 items may be defined for any one PEDSYS record a 35 6 REFORMAT April 19 1999 REPORT Program REPORT produces listings that are formatted so that information from one file is repre sented as a title or header that separates lists of data taken from one or more other files This format is particularly useful in displaying information about individuals taken from a Master File followed by a list of records pertaining to EGO taken from linked Data Files Introductory Display Selection of Header file EDSYS program REPORT Copyright 1992 SFBR REPORT produces listings that are formatted so that information from one file is presented as a title or header that separates lists of data taken from one or more other files Unlinked File EXAI PLE LOCUS Sub directory Enter number or name of file to use as HEADER information O to quit gt 2 A Standard File List is used to select the file from which header information is to be taken Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Enter number or name of file to use as HEADER information gt Here records from the Example Master Fil
268. files listed in its Directory File DBFILES appears April 20 1999 INFER e 23 3 AllLoci CandLoci D1S1656 D1S515 D1S3721 D2S1329 D2S326 D3S1229 D4S1582 D5S1466 D6S1036 D7S23 GGATIA4 J oO DSDWWN FL APOBpvu2a CAI ErrorDemo G6PD Enter a file number or name gt Here any single locus may be selected by entering its corresponding file number 3 18 Command sequences that follow are the same as those outlined above for unlinked files in the main Data Direc tory 3 Multiple loci listed in a special purpose file in the LOCUS Sub directory Alternately a pre defined set of loci file numbers 1 and 2 may be chosen The content of file 1 AllLoci is shown below APOBpvu2a CA1 ErrorDemo G6PD Note that the first record in the file must contain only the word FILELIST and that this record is 23 4 e INFER April 20 1999 followed by a list of file names exactly as they appear in the sub directory DBFILES In the example above we have included all locus files but the list may be constructed to include any subset as shown below APOBpvu2a G6PD Command sequences that follow are also the same as those outlined above for unlinked files in the main Data Directory Example 1 Inferring Codominant Phenotypes ADA locus ADA Phenotype is an autosomal codominant locus so that it is unnecessary to create a Genotype Phenotype Map File INFER proceeds by assigning ge
269. for a new subset of probands S to save P to create files containing PEDIGREES Enter Q to quit without saving This command is given if it is sufficient at this point to generate only lists of probands and ances tors in which case the program creates the appropriate files and terminates Output consists of a table of ancestor IDs numbers of proband descendants and the mean number of generational steps separating ancestors and probands file ancestor tab and separate files containing records of all probands file ancesego out and ancestors file ancesanc out Command P Save pedigrees connecting ancestors to their descendants This command re displays the list of ancestors selected along with options for creating and saving files containing selected pedigrees connecting ancestors to their proband descendants 6 ancestors have been found that are common to at least 2 probands Ancestor SEO PID ID065 1D042 ID045 ID034 1D047 ID062 No Pro Av No bands Steps 00 00 00 00 00 00 Enter SEQ IDs from the list above to creat files containing pedigrees that connect a single ancestor to its descendant probands Enter A to create a single file that contains one or mor Enter S to save files and exit probands gt a pedigrees connecting all ancestors and O to quit without saving For each ancestor selected a file is created that contains
270. for alteration or addition e Warning The carry over feature should be used with care as it is easy to inadvertently over write valuable information Once items have been selected ALTMASTR begins its data EDIT cycle First a request appears for the PID of the record to be changed Last entry in file is ID130 Enter Permanent ID of individual for which items are to be changed or RI to change mode of entry gt ID069 lt When this ID is entered the following display appears with the cursor positioned at the first item to be modified Enter items below as prompted one or more spaces to blank an item RETURN for next item or to advance to next step gt ID069 lt Ego s PID gt 19961013 lt Birth Date YYYYMMDD gt ID054 lt Sire s Permanent ID gt ID068 lt Dam s Permanent ID gt M lt Sex M F or U gt lt Exit Date YYYYMMDD gt O lt Exit Code gt lt Mate s Permanent ID 5 2 e ALTMASTR April 20 1999 The cursor moves automatically to a new line when entry of values for each item is completed Entry of RETURN as the initial character of any field leaves the current value unchanged important in the carryover feature entry of an initial blank character will erase the entire field When all items have been completed or if an initial square bracket has been entered in the initial position of any field the new values will be displayed for confirmation and the opportunity is
271. g data items typically an Ego ID Enter C to continue gt Here Ego PID has been selected as the identifier which determines sets of input records from which data items will be extracted and combined onto a single output record e Option Sorting Input Records within Sets Next an opportunity is provided to sort records within sets This will determine the order that items will eventually appear on the combined record April 19 1999 COMBINE e 11 1 3 Hemoglobin Level 4 INTERNAL POINTER 1 Ego 2 Sample Date COMBINE Sort within groups File MASTER XMP Record sets will be defined as marked above Optionally enter one or more numbers corresponding to items by which records will be sorted within sets precede with D for descending order Enter C to continue to next step gt 2 In this example Sample Date Item 2 has been entered for sorting in ascending order Note that the key item previously selected in Step 1 to define record sets Item 1 Ego PID is preselected in this display The option of sorting within sets may be skipped Step 2 Selecting Items to Include on Combined Output Records Next items that are to be included on the combined output record are selected 3 Hemoglobin Level 4 INTERNAL POINTER 1 Ego 2 Sample Date COMBI GB XI Select items to include File MASTER Enter numbers corresp
272. g display appears Sort input file by pedigree ID and sibship Y N gt Subsequently the program begins execution Notes on FISHER and MENDEL output e Because its records are not all the same length translat tab is not strictly speaking a PEDSYS Data File In the case of standard FISHER and MENDEL output however records containing pedigree data are formatted identically after header records have been removed and Code File transtab cde is provided to describe their structure See Appendix B Program TRANSLAT Format Translations page B 6 for more information on standard FISHER and MENDEL formats e The SFBR version of the standard FISHER output includes Code File transtab cde in the output file along with the FISHER output as selected above as well as several other records needed to control the shell program See Appendix B Program TRANSLAT Format Translations page B 7 for an example of FISHER SFBR output 7 PEDSYS to S A G E REGC format S A G E REGC requires a leading constant on each input record identifying it as belonging to a par ticular data set A query requesting this item appears after records have been ordered by Pedigree ID Enter a constant up to 5 characters to be used as Study ID gt LPDO1 Next the program proceeds to selection of quantitative phenotypes EGO Permanent ID ADA Phenotype 11 EGO SEQUENTIAL ID Sire s Permanent ID APOB Pvu2a Genotype 12 SIRE S SEQ Dam s Permanent I
273. genotypic data and or from keyboard entry Choice F Genotype Phenotype Map Data Read from File If choice F selection of a file containing an autosomal codominant locus is selected a File Selection display sequence appears from which a locus file is chosen June 10 1999 GENOMAP e 21 1 Select file containing locus Unlinked File EXAI PLE LOCUS Sub directory Enter number file name R to reselect mode of inheritance O to quit 327 Here the Example Directory has been selected Linked Files Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Specify file containing genotypic phenotypic data gt 2 the Markers Quant P types file 1 Ego ID 3 APOB Pvu2a Genotype 5 APOAI Level 2 ADA Phenotype 4 Tot Ser Cholestero GENOMAP Select locus File QUANTGEN XMP Enter number above corresponding to locus or enter RETURN to select another locus file gt 2 and the ADA Phenotype chosen 1 ADA Phenotype GENOMAP Select locus File QUANTG Is this correct gt Y If this is not correct entry of N the following display appears giving options to delete D re place R or add a table entry 21 2 e GENOMAP June 10 1999 1 ADA Phenotype ENOMAP Source of alleles File QUANTG to DELETE an item to REPLACE an item to ADD an item to CONTINUE to next step
274. gits preferred Optional Character Data Type preferred e Choice 2 The same input items as given for Choice 1 plus an item containing a permanent ID to be indexed are required to produce a Master File with additional indexed individual e Choice 3 Only the first three items in the table are required to index EGO FA and MO without producing a Master File e Choice 4 Only an item containing a permanent ID to be indexed is required in this case se Notes on Output Record Format e Choice 1 INDEX produces Master File records formatted as shown in the table below The first 12 items of the record are fixed in position while the remainder follow in an arbitrary order largely dependent on the order of items specified by the input Code File Items 1 11 16 19 and 20 are invariant in length while others may vary within limits specified in the table Items 1 11 as well as Pedigree Identification Number and Generation Number Items 19 and 20 in the table are family data derived during execution of the program A valid Master File can be created without specifying an Exit Date but this practice should be avoided if possible see Notes on Master File Record Format in Appendix A Pedigree Identification Number and Generation Number are added automatically Output records will also include additional items present in the input file Twenty standard items of a Master File are formatted as shown below 22 6 e INDEX April 19 1
275. go s records that appear in a Multiple entry Target file whether the latter is linked or unlinked In most cases it will be best to define an unlinked Multiple entry file as the Target rather than the Donor file e The command line shortcut with two input files program name followed by a blank the Target filename another blank and the Donor filename may be used to start this program Example merge sort out subset out Files Input Any two PEDSYS files having associated Code Files Recursive use of output files is permit ted that is file merge out nomergel out or nomerge2 out may be used as input to program MERGE Output merge out contains records in which items have been assembled from both Target and Donor files Optionally the output file may also contain records from the Target file for which no entries were found in the Donor file merge cde defines the record structure of merge out nomergel out contains records from the Target file that have no corresponding entry in the Donor file The Key Item is added automatically to records in this file April 19 1999 MERGE e 28 5 nomerge2 out contains records from the Donor file that have no corresponding entry in the Target file The Key Item is added automatically to records in this file nomergel cde and nomerge2 cde define the record structure of nomergel out and nomerge2 out respectively Program limits Records in Target and Donor files must contain identical Key I
276. gram TRANSLAT is used to translate between PEDSYS and other record formats including Pedi gree Draw and character delimited field format Introductory Display EDSYS program TRANSLAT Copyright 1992 1999 SFBR TRANSLAT converts between PEDSYS and other record formats CHARACTER DELIMITED FIELDS 1 PEDSYS to delimited field 2 Delimited field to PEDSYS EDIGREE DRAW 4 4 Use PREPDRAW for Version 5 0 3 PEDSYS to Pedigree Draw 4 4 4 Pedigree Draw 4 4 to PEDSYS EDSYS format to 5 FISHER 8 CRI MAP 11 SOLAR MIX 6 MENDEL 9 PAP 7 S A G E REGC 10 LINKAGE Enter number corresponding to type of conversion required or Q to quit gt RECIPROCAL CONVERSIONS 1 PEDSYS to delimited field When PEDSYS to delimited field format translation is chosen Standard File List Displays appear from which the file to be translated is chosen Once a file is selected and items have been chosen the following display appears from which a translation format is chosen Convert MASTER XMP from PEDSYS to character delimited field format TAB character Comma Single blank character Other delimiter may be 1 to 3 characters Enter number corresponding to type of separator to use as item delimiter gt 1 Enter single or double quote or to enclose character data RETURN otherwise Use CODE XMP Item Labels to create co
277. gree Draw output ATERNAL SIBSHIP SIZ ate s Permanent ID FULL SIBSHIP SIZI PEDIGREE NUMBER EGO Permanent ID GENERATION NUMBER Birth Date YYYYMMDD Ego ID Sire s Permanent ID ADA Phenotype Dam s Permanent ID APOB Pvu2a Genotype Sex M F or U Tot Ser Cholestero Exit Date YYYYMMDD APOAI Level Exit Code EGO SEQUENTIAL ID SIRE S S DAM S SE FIRST OFFSPRING SEQ EXT PATERNAL SIB SI EXT MATERNAL SIB SI EXT FULL SIB SEQ UMBER OF OFFSPRING PATERNAL SIBSHIP SIZ 0 0 JU amp ND H JO O1 amp NN H EPDRAW Palette 1 Standard types luo pl ter IF gt enter lt ItemNo gt lt Operator gt lt Test gt THEN SYMBOL lt symbol gt EXAMPL IF gt 1 EQ ID045 THEN S I IF gt 2 EQ ID055 AND 3 EQ ID065 THEN SYMBOI ter H for explanation and shortcuts C to continue Deceased E Stillbirth I Proband M Adopted Affected F Abort spont J Monozygot twin N Parents unmarr Pregnancy G Abort thera K Dizygotic twin O Parents separat H Lived lt 1 day L Zygosity unk P Parents divorc iscarriage Last entry IF 18 EQ 1 THEN SYMBOL A IF gt 12 eq IDO15 then i Here the standard deceased pattern a diagonal line drawn through the basic symbol has been selected and will be assigned to each individual in the pedigree that ha
278. gt If an unlinked file is used choice 1 above it must contain PIDs of Ego and Ego s parents and Ego s sex This file must then be used as input to program INDEX with the option to create a Master Pointer File selected When an unlinked file has been selected the program compares its Code File with entries in CODE STD for standard mnemonics EGO or ID FA or SIRE MO or DAM and SEX If the Code File contains these mnemonics the following instruction appears Use of an unlinked pedigr file requires that the file be in Master File format that is it must be indexed and have associated with it a Code File and a Master Pointer File such as INDEX MPT Enter the name of the pedigr file to use gt index out Enter the name of the code file for index out or enter RETURN for index cde the name of the Master Pointer File or enter RETURN for index mpt Failure to find a Master Pointer File results in the option to enter another file name or to return to the Initial File List display When a Master File or indexed pedigree file with an appropriate Master Pointer File has been selected an Item List Display appears from which items may be selected for inclusion in the output files generated by the program Once this is done the following display appears from which the method of constructing pedigrees is selected May 19 1999 MAKEPED e 27 1 MAKEPED will construct pedigrees in two ways
279. gt lt mne4 gt not valid mnemonic 11 where lt ego gt is the PID of the record to be updated in lt filename gt UPD and lt mne1 gt etc are mnemonic words identifying the item in file lt filename gt UPD This error may occur either when adding a new individual or when making changes to a record previously entered in the Data File Probable cause is a change made to lt filename gt cde since the time it was used with ALTERDAT 38 2 e SETDATA April 20 1999 The most convenient way to correct this error if it has occurred infrequently is to use program ALTERDAT to re enter the changes that failed and then re run SETDATA using the same Code File with both programs If the error has occurred many times it may be easier to start over re running SETDATA using the correct Code File and the previous Update and Data Files Since these files are now named lt filename gt OUP and lt filename gt OLD respectively they will have to be given their original names lt filename gt UPD and lt filename gt lt ext gt respectively before they can be used with SETDATA Group 2 PID Conflicts Changes and additions to Data Files are prohibited if errors or conflicts are found in Permanent IDs PIDs of records in the Data File containing records to be changed These errors are reported as follows lt ego gt Not added record already exists in Data File 21 lt ego gt Not found in Data File entry not changed 22 where lt
280. h and Unix machines s 22 10 e INDEX April 19 1999 INFER Program INFER infers unknown phenotypes and genotypes from phenotypes or genotypes of rela tives The program examines each offspring father mother triplet and when possible adds missing alleles and genotypes according to the Mendelian laws of transmission An error is reported when an inconsistency between Ego and a parent is found When all triplets have been examined the program starts through the pedigree again making assignments on the basis of genotypes inferred in the previous iteration The entire pedigree file is re examined repeatedly until no more assignments can be made by examining triplets The file is again re examined this time for inconsistencies revealed by including the grand parental generation and by checking the distribution of alleles within entire sibships Introductory Display EDSYS program INFER Copyright 1992 1999 SFBR FER infers unknown genotypes from phenotypes or genotypes of relatives Unlinked File merge out EXAI PLE LOCUS Sub directory Enter number of the file or directory to use gt 3 Loci may be selected for analysis in several ways 1 Anunlinked file containing genotypes or phenotypes for one or more loci It is often convenient to organize multiple genotypes and or phenotypes on the same record An ex ample of this organization is given by file merge out choice 2 above in which gen
281. h a dash in individuals ID015 ID045 and ID056 indicating that the X linked G6PD allele determining their phenotype is not yet known INFER starts with this information and iteratively attempts to fill in the missing types according to the Mendelian laws The results can be seen in the next diagram April 20 1999 INFER e 23 9 ID038 ID056 A 1D077 AB ab ID067 B bb Pedigree DrAw Inferring from Genotypes DNA marker types are typically referred to as genotypes rather than phenotypes INFER inter prets marker data as genotypic only if the mnemonic word GENO or G TYPE appears as one of the last three mnemonic words associated with the Code File entry The program proceeds in the same fashion as it does when making inferences from codominant phenotypes Output Output of INFER may be directed optionally to files infer1 out and or infer2 out File inferl out con sists of all records from the input locus file in their original order Each record contains input items in their original order with the inferred phenotype or genotype appended at the end An example of a display from program BROWSE showing contents of infer1 out for the ABO locus file is shown below 23 10 INFER April 20 1999 inferl out Top record 1 32 1 2 3 ID ABO ABO PHENO SAMPLE D015 R236 D019 R240 D034 R238 D038 R216 D042 R218 D045 R230 D047 R232 D049 R248 D054 R234 D055 R222 D056 R214 D061 R212 D062 R224 A B
282. haracters sought For example if 12 eq 5 then g if 12 eq ID02 then h if 12 eq 0 then i The first command assigns a symbol type to any PID ending in the numeric character 5 the second command makes an assignment to any PID ending with numeric characters 20 to 29 while the third command assigns a symbol to any PID containing the numeric character 0 Substring values may be tested in multiples as well if 12 EQ 071 049 045 034 then s a 34 10 e PREPDRAW May 4 1999 Here the numerical portion of EGO PID is tested for four specific values These examples illustrate the point that substring searches may be done on any field no matter how the item Data Type is defined in the Code File C D I or R Substring searches are slow and should be avoided when rapid output is needed e Equivalences As a convenience several command elements have been given equivalent alternate forms These are GT LT EQ NE GE LE I v equal sign lt gt or gt lt must be matched pairs or or In addition the assignment statement has two short forms so that the following commands are equivalent if 12 EQ ID015 then symbol a if 12 EQ ID015 then s a if 12 EQ ID015 then a Symbol Selection Table Format The Symbol Selection Table consists of records containing command sequences formatted as written at time of input Shown below is the table resulting from the changes specified in the examples sho
283. he first page of the input record is displayed as two lines of text each up to 78 characters long below an Input Ruler The colon symbol in the Input Ruler designates a character on the input record that has not yet been assigned to a PEDSYS data item as a visual aid every fifth unassigned character is marked with a stroke 1 Characters that have been assigned to a PEDSYS item are marked with an underline character _ while characters on the input record that are not to be included as PEDSYS items are marked with a skip symbol In this example the record requires only one page and its second line of text does not extend across the screen Below the data display are instruction and command lines which may vary depending on which operations are available The consequence of choosing the options shown is as follows 24 2 e ITEMIZE April 20 1999 A ASSIGN characters to Item Defining the first or any item consists of a determining the number of characters starting at the beginning of the unassigned portion of the input record that constitute a PEDSYS data item and b assigning a Data Type and single mnemonic to the newly defined item From the example above it can be seen that an a has been entered at the command line which produces the following display ER XMP Record 1 of 32 Length 95 0ID06119720309 M1998042 O1ID042 Item 1 gt 5 lt Enter number of characters to be assigned to this item 1 95 g
284. he unknown date may be represented by a full field of nines 99999999 or 9999999 If dates are repre sented by year alone 9999 may be used but not 999 which represents the year 1999 in our abbreviated format Nines may not be used to represent unknown or missing month or day when year is known e The table below lists various configurations of the date field and their interpretations by program AGE Year Month Interpretation Full representation Day estimated Month and day estimated Skipped Invalid LR A A D D D D Q o lc YH lc NYS where represents data present represents missing data 3 4 e AGE June 12 1999 Interpretation a Full representation of year month and day An error message is written to age err if Non numerical characters other than blanks are found in the record or are entered from the keyboard after the letter D Embedded blanks are also invalid Month falls outside the range 1 12 or day falls outside 1 31 with exceptions for missing ele ments noted below Year is present and month and or day is represented by nines b When year and month are present but day is missing expressed as blanks or zeros an age cal culation is done using day 15 as an estimate of mid month c When year is present but month and day are missing that is both fields are filled with blanks or zeros an age calculation is done using 30 June as an estimated mi
285. he CD ROM consists of locating and opening the MAC folder opening the PedSys folder and dragging the PedSys PPC or PedSys 68K folder to your hard drive depending on whether the tar get system is a PowerPC or 680x0 based Macintosh Each of these folders contains an applications folder PedSys Progs and Example a small data folder e The SFBR web site provides PEDSYS in four Self Extracting Archive sea files for both old and new systems Archive file names for the PowerMac edition are of the form PedSysPPC1 sea while equivalent archive names for Macintosh 680x0 edition are of the form PedSys68K1 sea The first archive file contains the Data Management applications and example files in a folder called PedSys Open double click the sea file to start the extraction process and specify a hard drive location where the archive folder PedSys68K1 Folder will be installed When the extraction pro cess is complete for the first archive file the PedSys folder will be present in this archive folder The PedSys folder contains two others PedSys Progs which stores applications and support files and Example a small data set that can be used to test the system Archive files 2 4 contain the remaining applications which will also be stored in similarly named archive folders when extrac ted Drag these applications to PedSys Progs to complete the installation About 18 MB hard drive space is required for the full installation The User Manual is contai
286. he output record Right or left JUSTIFY items by preceding item number with gt or lt Preceding item number with U or L or LOWER sets all alphabetic characters in the selected field to UPPER case Enter C gt to continue item selection Enter P to page April 19 1999 and REFORMAT item by preceding item number with F This feature permits in crease or decrease of field width and subdivision of item A field of BLANKS may be entered with command B Field width item label and mnemonics are requested A CONSTANT fixed field of characters may be entered with the K command The string must be surrounded by single or double quotes Item label and mnemonics are requested A RANDOM fraction is added at the end of the record with the R command A 1 8 digit integer seed is requested An ordered SEQUENCE number is appended to the record with the S command JOIN two or more items by entering this command and selecting items to be joined from the redisplayed Item List Enter RETURN to continue selecting items gt Notes e Program REFORMAT permits items to be removed simply by not selecting them or duplicated by repeated selection as well as rearranged in the output record e The justification feature works for all data types but is normally used only with character data type C Left justification of integer
287. he structure of records in its accompanying Data File Use program REFORMAT to change the structure of records in a Data File REFORMAT alters the data records and automatically produces a Code File named reformat cde that reflects the changes A common mistake made by first users of PEDSYS is to try to change the format of records in a Master File or Data File simply by changing the definition of these records in the associated Code File This does not work Changing a Code File by itself does not change the contents of records in the file with which it is associated e Changing Item Labels and Mnemonics affects the description of items as read from screen and output display which may be crucial for understanding and interpreting the meaning of stored data but such changes do not alter the physical contents of the records nor do they affect the operation of the PEDSYS programs that use them Likewise simply adding or deleting items or changing the specification of item field widths in a Code File does not change the actual structure or content of records in the associated file Moreover April 19 1999 CODE 10 5 PEDSYS programs require a Code File to determine the format of records in any input file Thus if the Code File reflects changes in structure that have not been made to the file it is supposed to describe it is unlikely that programs will accept input without error and termination e Also important The order of items entered f
288. here is a sufficient number of characters in the input record that have as yet been unassigned to data items If the width of an item cannot be increased because there are not enough unassigned characters remaining it will be necessary to delete or decrease the width of one or more items so as to accommodate the frame shift S SUBDIVIDE an Item The S command is used to subdivide an existing item without changing its width Entry of S lt n gt where lt n gt is a number corresponding to the item to be subdivided produces the following display April 20 1999 ITEMIZE e 24 5 Subdivide SKIP Enter number of characters to be assigned to this item 1 32 Enter the Data Type of the item C I or R or S to skip Enter a single mnemonic for this item Here subdivision of Item 4 initially designated as a skip field has been selected and is displayed alone on the screen as an unassigned string Definition of items proceeds in the same way as described for the original assignment of data characters Here also the first five characters are defined as integers and given the mnemonic KID1 which results in the following display Subdivide SKIP Enter number of characters to be assigned to this item 1 27 This pattern is repeated for subsequent assignments Item numbers are incremented and displayed as items are defined When all characters have been assigned the screen returns to a full command display with all items nu
289. icitly identified in screen displays Multiple entry Data Files are normally created and updated with the PEDSYS program ALTERDAT although any text editor can be used providing that pointers are maintained correctly a risky assump tion Programs ALTERDAT and DATALINK assign and process internal pointers automatically Linked Data Files conventionally are named lt FILENAME gt lt EXT gt where lt FILENAME gt is an arbit rarily chosen name identifying the data set upper case only and lt EXT gt is an extension identifying the population For example MARKERS XMP is the name of one of the Example Data Files distributed with the PEDSYS package 4 Code Files PEDSYS programs require information about the structure of the records they process that is the format description and data types of the items they contain This information is passed to the programs from a special purpose Code File associated with each Master and Data File Although we refer to Master Code Files and Data Code Files the basic composition of the two types is the same The first record of a Code File contains a label that identifies the file defined by the Code File Subsequent records contain descriptors that define the format and contents of items in the Master File or Data File All records in a Code File must be exactly 54 characters long Code Files normally are created with the PEDSYS programs CODE or ITEMIZE although any text editor can be used if care is t
290. ield width data type and the exact spelling of the mnemonic words are invariant in some Code Files See Master Files Data Files and CODE STD in Appendix A and documentation for Program INDEX for details e A useful way of checking whether or not a Code File fits the Data File is to run program BROWSE or SHOW choosing the Unlinked File category and then specifying the Data File name and code tab as the associated Code File If a few pages of the screen display are correctly formatted it is likely that the Code File was properly constructed If however records are out of alignment immediately run program ITEMIZE with the same input files ITEMIZE will readily expose errors in field widths etc and makes it easy to correct them Files Input 1 Console and optionally a previously constructed Code File 2 Any Code File when starting program in Edit Mode Output The new Code file may be saved either as 1 code tab 2 lt filename gt where lt filename gt is the either a newly chosen name or the name of the Code File selected as input for modification Program limits Up to 100 Code File Descriptor Records each corresponding to an item in records of the associated Master File or Data File Fa 10 6 CODE April 19 1999 COMBINE COMBINE produces single new records each containing one or more values extracted in sequence from a Data File containing sets of records defined by a common identifier The most obvious use o
291. igree items The program also searches for a Master Pointer File identified by a matching file name and the extension mpt In the example above age out was created directly from the Example Master File so that pointer file MPOINT XMP could be used If no Master Pointer File is available it may be neces sary to use the unlinked pedigree file as input to program INDEX with the option to create a Master Pointer File selected Failure to find a Master Pointer File results in a request for another file name When a Master File or indexed pedigree file has been selected an Item List Display appears from which items may be selected for inclusion in the output files generated by the program EGO SEQUENTIAL ID 9 PATERNAL SIBSHIP SIZ I Date YYYYMMDD SIRE S SEQ 10 MATERNAL SIBSHIP SIZ Code DAM S SEQ 11 FULL SIBSHIP SIZE s Permanent ID FIRST OFFSPRING SEQ 12 EGO Permanent ID EDIGREE NUMBER PATERNAL SIB SE 13 Birth Date YYYYMMDD ENERATION NU MATERNAL SIB SE 14 Sire s Permanent ID EXIT BIRTH FULL SIB SEQ 15 Dam s Permanent ID ER OF OFFSPRING 16 Sex M F or U 1 2 3 4 5 6 7 8 ESTOR Items to be included File age Enter numbers corresponding to items shown above in the order they are to b included Enter A to include all items or C to continue gt Next the source of proband IDs m
292. ile gt If a new Data File is to be created from information stored in lt filename gt UPD the following display will appear Data File NEWFILE XMP will be created and update file N E UPD will be renamed NEWFILE OUP Enter C to continue or X to EXIT program without creating Data File gt In this example Data File NEWFILE XMP has been specified in the File Selection sequence April 20 1999 SETDATA e 38 1 Error Messages and Displays Program SETDATA is usually run as the last step in permanently updating or creating PEDSYS Data Files Considerable effort has gone into preventing errors from being incorporated into the data Protection from permanent damage is provided at two levels Level 1 Errors that affect single records are recorded in the setdata err file and the record in question is not updated Level 2 Backup copies of original input files are created so that it is always possible to discard incorrect changes and return to an earlier version of the data Here are the error messages that may appear in setdata err and the measures that should be taken to correct them For convenience errors are grouped into three classes Group 0 Unprintable Characters In order to prevent unprintable characters from being added to the Data File records each new entry in lt filename gt UPD is scanned for characters with ASCII decimal code values less than 32 or great
293. ile requirements are Sequential IDs of EGO FA and MO and Pedigree ID number The pro gram runs automatically if mnemonic PEDNO or Standard Mnemonics for IDs SEQ FSEQ MSEQ EGO FA and MO for humans SEQ SSEQ DSEQ ID SIRE and DAM for nonhumans are found in the input Code File Otherwise an opportunity is provided to designate required items labeled with nonstandard mnemonics When a pedigree file has been chosen a request for an alternate output file name appears if the default file peelseq tab is not wanted Enter output file name or RETURN for default name peelseg tab gt The program then begins execution Format and content of output records from file peelseq tab are illustrated in the following table Founder No ID ID Cut Status of of Kid i Kid set Link Link FA MO Kids 1 3 Size ID ID 0 0 3 16 18 2 12 10 The first five variables are invariant but No of Kids variable i is followed by i offspring IDs and Cut set Size j is followed by j Link IDs This structure means that the number of variables in a record will vary depending upon the number of offspring and the cut set size of the nuclear family it represents Linking individuals are those that connect a nuclear family to other parts of the pedigree that have not yet been included in the peeling sequence At least one of these linking individuals is a member of the nuclear family in question who is also a member of another nuclear family not yet included in the
294. in pairs from records in a file This option likewise results in a request for the source of pairs for which calculations will be made Here a 1 has been entered specifying that all opposite sexed pairs will be formed and analyzed Proband IDs entered from the keyboard Prior to entry the form of the IDs Permanent or Sequential must be specified This is followed by requests for pairs of IDs 25 4 e KINSHIP April 20 1999 Enter RETURN if individuals ar Sequential IDs gt gt ID034 lt ID 1 gt ID054 lt ID 2 gt ID069 lt ID 1 gt ID067 lt ID 2 lt ID 1 Enter pairs of Permanent IDs R identified by Permanent IDs Here two pairs of PIDs have been entered Proband IDs read from a file ETURN alone terminates entry Or SP LE by Selection of a pair of items containing the proband IDs is made from a Standard Item List Display EGO Permanent ID Birth Date YYYYM Sire s Permanent I Dam s Permanent ID Exit Date Exit Code M F or U YYYYMMDD ate s Permanent ID EDIGREE NUMBE ENERATION NU PROBANDS Identify KINSHIP File subset out continue gt Enter a single pair of numbers above corresponding to Proband Ids C to Here measurement of kinship coefficients between Ego and mate both designated by Permanent IDs has been specified Calculations will be done for Ego
295. in 1 Rec11 Sample Date 21 Rec7 Hemoglobin 1 Rec12 Sample Date 22 Rec8 Hemoglobin 1 Rec13 Sample Date 23 Rec9 Hemoglobin 1 Recl Hemoglobin Leve 24 Rec10 Hemoglobin Rec2 Hemoglobin Leve 25 Recll Hemoglobin Rec3 Hemoglobin Leve 26 Rec12 Hemoglobin Rec4 Hemoglobin Leve 27 Rec13 Hemoglobin Ego Recl Sample Date Rec2 Sample Date Rec3 Sample Date Rec4 Sample Date Rec5 Sample Date Rec6 Sample Date Rec7 Sample Date Rec8 Sample Date x1 1 2 5 4 5 6 F 8 9 I Oo O DSWNL CALC Sum N mean Std Dev Err File combine out Enter numbers corresponding to numerical values above for which a sum N and Std Dev Err are to be calculated Enter C to continue gt Once items have been selected the following display appears It may be desirable to substitute a pooled intra individual standard deviation SDs averaged across all records in calculations of the standard error when N the count of individual values is very small Enter a maximum N for which this adjustment will be made to the standard error Enter RETURN to skip this adjustment gt 2 Here the adjustment has been selected for calculations of standard error for any record where the number of measurements N lt 2 To see the effect of the adjustment compare the two displays below The first shows selected results for the unadjusted standard deviation calc out Items 32 Top record 18 27 1 28 29 30
296. in fact an entry for that individual in the newly selected file A warning message will appear if there is no entry for that ID in the file Thisoption can be used only when a Master File or linked Data File has been selected This command results in a return to the File List from which a new file or set of files may be selected for display in the usual manner H Entry of H produces the following help display pages To set the record that will appear at top of page enter a Permanent ID S followed by EGO Sequential ID or followed by a number representing a record s position in the file and then hit RETURN enter RETURN for steps of one precede To page BACKWARD through file lt n gt for steps of lt n gt To page FORWARD through a file RETURN with lt n gt for steps of lt n gt pages precede RETURN with for steps of one To shift the window RIGHT or LEFT enter gt or lt for shifts of one item gt lt n gt or lt lt n gt respectively for shifts of lt n gt items To set the item that will appear in the left most unlocked column enter I lt n gt where lt n gt is the item number then hit RETURN Enter L to select columns for LOCKED display that is fixed in position on the left hand side of the screen despite horizontal movement of the dis play window Enter P to page Enter C to return to data display gt and
297. in with command characters I or i and P or p To circumvent this possibility the following alternates may be used lt n gt maybe substituted for S lt n gt or s lt n gt lt n gt ee Ikn gt or i lt n gt lt n gt 6 sali P lt n gt or p lt n gt In the example just given specification of Sequential ID 10 would be 10 to distinguish it from PID S10 Likewise 5 may be substituted for i5 to specify that Item 5 be placed in the left most unlocked column and 2 may be used in place of p2 to specify the second display page where needed The default characters were chosen to speed up command sequence entry by avoiding the use of the keyboard shift key The alternates are available in all relevant PEDSYS programs To save screen space for data a maximum of two mnemonics per item are displayed in the header April 19 1999 SHOWDATA e 41 7 Files Input Up to five Linked Data Files or a single unlinked file with their associated Code Files Output Console screen 41 8 e SHOWDATA April 19 1999 SORT Program SORT performs a compound sort of records in any file for which an appropriate Code File has been constructed Introductory Display EDSYS program SORT Copyright 1992 1999 SFBR SORT performs a compound sort of records in any file for which an appropriate Code File has been constructed Unlinked File EXAI PLE LOCUS Sub directory Enter number file name or Q to quit
298. ing option is given Display grandparental genotypes Y N gt The following sequence then appears Tabulate separately by sex of offspring Y IN gt Enter minimum number of offspring per mating gt 1 If tables for individual parents are selected choices 1 2 above the following sequence appears in which genotypic data for the selected parent here the sire is defined Select type of segregation table to be constructed Separate tables for fathers identified by father s PID Separate tables for mothers identified by mother s PID Separate tables for parental pairs identified by both PIDs Combined table for fathers with same genotype Combined table for mothers with same genotype Enter number above corresponding to choice gt 1 Tabulate separately by sex of offspring Y IN gt n Enter minimum number of offspring per sire gt 2 37 2 e SEGCHECK May 21 1999 Select father s genotype 1 Heterozygous fathers only 2 Homozygous fathers only 3 Both types Enter number above corresponding to choice gt 3 Exclude matings that do not reveal segregation Y N gt The program then reads through the Data File to determine which alleles are present The following alleles were found for D1S 1656 G TYPE A B C D Enter RETURN to include genotypes based on all of the above E to select a subset Q to quit without executing gt If an e
299. ingle record for each individual Each record must contain minimally five of the last six items listed in CODE STD see The Standard Mnemonics File Appendix A These are No of Standard Data Item Characters Mnemonic Type Notes EGO Permanent ID PID 3 9 ID or EGO E may be numeric Sire PID 3 9 SIRE or FA may be numeric 10 December 1996 Creating a Pedigree Database 4 1 Dam PID 3 9 DAM or MO C may be numeric EGO s sex 1 SEX C coded M F U or 1 2 3 EGO s birth date 3 8 BIRTH or BIR D EGO s exit date 3 8 EXIT D optional but useful It is important that these items conform to the specifications of the CODE STD Order of the items is not important Creation of the files necessary for a minimal Pedigree Database is done in four steps Step 1 Create a Code File for the new PEDSYS Master File by running program CODE choosing Create Mode and entering H or N to specify the human nonhuman Master Code File option CODE will automatically enter whatever information it can that is required by the Master File format and will request entry of optional labels mnemonics field lengths and data types When entry is finished the output file should be named CODE lt EXT gt where lt EXT gt is the file extension identifying the population If you forget and give the file its default name of code tab it will be necessary to rename it Depending on the computer on which PEDSYS is installed this can be done with one of the fo
300. ion What follows here is a brief description of the concepts involved The SCCS control program uses an SCCS subdirectory created in each Data Directory containing a special copy of the files to be protected Each of these copies starts out with the original data but accumulates a dated history of all changes made as it is modified over time These history files as they are called keep the names of the original files but prefix them with an s for example MASTER XMP becomes s MASTER XMP History files are assigned read only access and may be updated only with the SCCS edit command which creates a single editable working copy of the history file A user with SCCS write privileges may modify this copy for example with program ALTERDAT The history file itself is automatically locked while the working copy is being updated When changes have been completed the s version is updated and the working copy automatically deleted The SCCS get command is then used to create a non editable read only working copy of the history file This copy is the one accessed by PEDSYS users who do not have Data File write privileges In addition to the file locking feature SCCS also makes it possible to audit past changes made to a file An excellent short explanation of SCCS has been written by Peter Collinson in the October 1991 issue of SunExpert magazine pp 34 39 Fe 4 Setting Input Output Directories June 10 1999 INSTALLATION and SETUP SOLA
301. ions to use in allocating temporary work files some of which may be larger than the source files being processed e A PowerPC based Macintosh with 16 MB of internal RAM or a 680x0 based Macintosh with a floating point unit FPU and 8 MB of RAM Virtual Memory may be activated to allow appli cations requiring more memory to run successfully For 680x0 based Macs which do not include a FPU as standard equipment SoftwareFPU may be used to provide emulation Version 3 04 has been included on the PedSys 68K release disk it is offered as shareware by John Neil amp Associates for a registration fee of 10 More information is available at http www jna com The RAM requirements for individual programs are based on a Master file record limit of 30 000 rec ords This allows most PEDSYS applications to run in a 1 2 MB memory partition although programs such as Index and Kinship require a 4 6 MB partition The Suggested Memory sizes set for each application were determined by experimentation If a PEDSYS program terminates abruptly when processing large files or otherwise indicates that too little RAM is available increase its Preferred Memory allocation under the Finder using Get Info command on the File menu and rerun Use the memory partitions display in the About this Computer window as a guide to adjusting the memory required by a particular application e Support Files e The first two support files are provided in the PedSys Progs folde
302. is entered an opportunity is given to select a subset of the alleles shown If the Data File contains inferred phenotypes or genotypes the following option is given Tabulate without distinguishing between known and inferred genotypes Tabulate known and inferred genotypes separately in same table Exclude inferred genotypes from tables Enter number of choice above gt SEGCHECK then proceeds to construct segregation tables Notes e SEGCHECK requires unambiguous representation of zygosity which means that tabulation is limited to a codominant autosomal phenotypes or b genotypes Segregation tables for domi nant recessive and X linked phenotypes can be generated however by transforming these rep resentations to their genotypic forms with program INFER File infer2 out can then be used as unlinked input to SEGCHECK e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example segcheck subset out May 21 1999 SEGCHECK e 37 3 Error Checking Error detection in SEGCHECK is limited to identifying discrepancies between parental and offspring phenotypes or genotypes When such a discrepancy is found a record is written in file segcheck tab containing PIDs and phenotypes Algorithm R H King L Freeman Shade Files Input A Data File with records containing genotypic or phenotypic data with associated Code File and a s
303. ise it creates and saves a new copy e You may have more than one PATHWAY file each with different contents on your system This is because copy of PATHWAY is created in any directory used as the Current Working Directory sa E 8 INSTALLATION and SETUP Solaris 2 5 June 10 1999 Appendix F INSTALLATION and SETUP Apple Macintosh OS In this appendix we describe directory organization installation procedures and file access and permissions for the Apple Macintosh OS 7 1 8 1 1 Directory Organization The basic scheme assigns executable program files to an independent Program Directory which is kept separate from any number of Data Directories which in turn may contain one or more sub directories These directories are set at the same hierarchical level below a PEDSYS root directory as shown in the following diagram PEDSYS Root Directory A PEDSYS PEDSYS PEDSYS Program Directory Data Directory Data Directory y y DN Sub directory Sub directory Sub directory Sub directory a The PEDSYS Folder The Macintosh folder corresponding to the PEDSYS root directory contains only the Program Folder and one or more Data Folders here the Example folder PEDSYS PEDS YS Progs Example June 10 1999 INSTALLATION and SETUP Macintosh OS F 1 The Macintosh Program Folder contains the following files S2 items CH Age a AlterDat Ha Altmastr Ha Ancestor Ha Append H Browse Bi Calo H Code Ha Combine
304. isplay window will be located in the monitor which contained most of the original window area F 6 e INSTALLATION and SETUP Solaris 2 5 June 10 1999 Multi tasking Under certain conditions most PEDSYS applications can be run concurrently and share access to the same files in the Data Folder The primary requirement is that the Allow Multiprocessing item in the Options menu of PedSys be checked the default otherwise only one application at a time is allowed to launch The second requirement is that there be enough available RAM to support multiple program partitions A third requirement is the program not be one of eight File Management programs AlterDat AltMastr Code DataLink DBFiler DelRecs SetData and SetMastr which update Master Data or Support files These applications require exclusive access to the files they are updating so they are not allowed to run unless all active PEDSYS applications have terminated A program is terminated by selecting Quit from the File menu by closing the display window or by entering Q or X for Quit Exit when this option is offered by a program These methods return control to PedSys Entering Command period Control C or Command C also ends an application but returns control to the Finder Editing Text Files The PedSys application provides a simple ASCII text editor for viewing files and saving changes It is invoked by selecting Open on the File menu and specifying a file n
305. it program Note e The command line shortcut with two input files program name followed by a blank one input filename another blank and a second input filename may be used to start this program Example append sort out subset out Files Input Two or more Master Files or Data Files lt filename1 gt lt ext gt and lt filename2 gt lt ext gt each having the same format Corresponding Item Descriptor Records of all Code Files must specify identical width and data type mnemonic and description fields need not be the same Recursive use of output files is permitted that is file append out may be used as input to program APPEND April 20 1999 APPEND e 8 1 Output append out contains the joined files append cde will be identical to the Code File of lt filename1 gt lt ext gt the first of the input files except that its label will read as much as will fit of lt filenamel gt lt ext gt lt filename2 gt lt ext gt lt filename3 gt lt ext gt where lt filename2 gt lt ext gt is the second of the two input files etc z 8 2 e APPEND April 20 1999 BROWSE Program BROWSE gives a direct display of records a screen page at a time from any PEDSYS file having an accompanying Code File BROWSE is in some ways similar to SHOWDATA but unlike SHOWDATA it is record oriented rather than individual oriented That is BROWSE displays rec ords of more than one individual in a file whereas the multipl
306. items but substitutes mnemonics ID SIRE and DAM for EGO FA and MO respectively 10 4 CODE April 19 1999 si Starting CODE in EDIT Mode When initial choice E for EDIT is selected the screen shown below is displayed from which the Code File to be edited may be chosen 1 Unlinked Code File 2 Example Enter number of the file or directory to use gt Choice of 1 from the list above results in a display of Code Files associated with unlinked Data Files Included in this list are code tab if it exists any file with a name in the form lt filename gt cde or the form CODE lt ext gt where lt filename gt is the name of the data file and lt ext gt is the file name extension Both upper and lower case characters will be shown Once the Code File has been selected editing begins The edit display and its commands process are the same as that described above except that the options provided for naming the output file are slightly different from those given when a new Code File has been created When a previously created Code File has been modified entry of s or x directs the program to save the output and exit Naming the output file depends on the origin of the input file Enter a name for this Code File RETURN alone to save output as code tab or R to replace examp cde gt Notes e VERY IMPORTANT NOTE Program CODE alters ONLY the Code File modifying the Code File alone does not alter t
307. ked left hand columns Enter C to continue gt In the example above EGO Sequential ID and EGO Permanent ID Items 1 and 12 have been allo cated to locked columns using common spreadsheet terminology at the left most side of the display The remaining items remain unlocked The result of this selection can be seen in the following display MASTER XMP Items 21 Top record 31 32 1 12 2 3 4 5 6 7 8 9 10 11 SEQ ID SSEQ DSEQ KID1 PSIB MSIB FSIB NKID PSIBSZ MSIBSZ FSIBSZ 31 ID124 29 24 32 30 32 ID130 31 30 0 0 Enter lt n gt or lt n gt for new page PID S lt n gt 1 32 or lt n gt 1 32 to set top row gt or lt lt n gt to shift window I lt n gt 1 21 to set window L to lock columns to switch files F to find H for help Q to quit gt Columns may also be locked in sequence from the left by entering L followed by an Item Number For example columns can be ordered in the same sequence as shown in the display above by entering L1 followed by L12 Items in locked columns form a subset of other items displayed and are positioned in order of selec tion from the left most boundary of the screen They remain visible in their locked positions despite subsequent horizontal shifts of the remaining items selected for display Locking is partic ularly useful for maintaining visibility of a PID while shifting horizontally across long records Any item not
308. le selected appears from which items may be chosen for inclusion in the output records generated by the program 1 Ego ID 3 APOB Pvu2a Genotype 5 APOAI Level 2 ADA Phenotype 4 Tot Ser Cholesterol TRIPLETS Items for EGO File QUANTGEN XMP Enter item numbers in the order they are to be included in the output record A to select all or C to continue gt Here the first file selected was the Markers Quantitative Phenotypes file from which the Tot Ser Cholesterol Phenotype has been chosen EGO PID has been preselected These will be the first items to appear on the output record Item List Displays of subsequent files appear in the order they are selected 46 2 TRIPLETS June 5 1999 1 Ego 3 Hemoglobin Level 2 Sample Date 4 INTERNAL POINTER TRIPLETS Items for E File HEMOGLOB XMP Enter item numbers in the order they are to be included in the output record A to select all or C to continue gt Here Hemoglobin Level has been selected from the Hemoglobin Levels file Note that EGO PID is not preselected here Once items for Ego have been chosen the following display appears Enter same items for SIRE as selected for gt y Enter same items for DAM as selected for SIRE y Here the same items selected for Ego PID Tot Ser Cholesterol and Hemoglobin Level have been selected for both parents Had an n been entered at ei
309. lected at the time the program is started starting in Edit Mode requires that a pre existing Code File be present CREATING a new Code File When initial choice C for CREATE is selected the following instruction appears Enter D to create a Code File for a Data File H to create a Code File for a Master File HUMAN population N to create a Code File for a Master File NONHUMAN population Option D Create a Code File for a Data File Entry of D at this point begins the process of creating a Code File for a Data File Enter TITLE of file with which Code File will be associated gt Tissue Inventory This entry 47 characters maximum will be stored as the Code File Label Record see Code Files Appendix A The entry may be a file name but since it is used as a title in screen and print displays it is usually preferable to enter a more complete or mnemonic description Consequently we find it advantageous to use a title such as Tissue Inventory here rather than simply TISSUES XMP CODE then begins a repetitive cycle of requests for information about each item to be included in the Data File records gt Animal ID lt Enter label for Item 1 or RETURN for next step lt Enter mnemonic 1 for this item to re enter lt Enter mnemonic 2 for this item to re enter Enter width columns of this item to re enter Enter data type of this item or re enter I for integer v
310. lects this limit and permits addition of only one Data File to DBFILES at a time ERROR Discrepancy between number of Data Files specified DPOINT lt EXT gt lt nfiles1 gt and in DBFILES lt nfiles2 gt where lt nfiles1 gt and lt nfiles2 gt are the respective file counts Records in the Data Pointer File contain a separate pointer field for each Data File linked to the Master File If the number of pointer fields does not match the number of Data Files listed in the Data File Count Record there is a danger that the correct order of pointers has been lost which could lead to serious damage to data To recover from this error it will be necessary to delete DPOINT lt EXT gt and DBFILES and to start the DBFILER DATALINK cycle from the beginning until all files are correctly linked and listed in DBFILES ERROR lt FILENAME gt lt EXT gt is already listed in DBFILE n This error occurs when attempting to add a Master File or Data File that is already listed in DBFILES sa Notes e We recommend using DBFILER for all modifications to the Directory File This is particularly important when adding or removing Linked Data Files which requires not only changes to DBFILES but also addition or deletion of the appropriate pointer field in the Data Pointer File DPOINT lt EXT gt e It is important to understand the conditions under which program DBFILER modifies actual file and directory content
311. les desired 2 minimum gt 4 Here a reduction to four of the six alleles found initially in the pedigree has been specified In Interactive mode the following display appears this step is skipped in Automatic mode D2S1329 Genotypes Current Start Alleles 6 6 Informative triplets 13 13 Allele Equivalence Triplets Heterozygotes Nuc Fams Lost Lost Affected to 0 0 0 to to to to to to to to to to to to to ba hange hange hange hange hange hange hange hange hange hange hange hange hange hange hange 0 0 JU amp N EH PRP rrer Ow amp ND h C E C 6 C E E C E C C E C AO Am mHATARnQAQ Gi bi Hi gt gt OU WE gt OU amp Ni WNNNNHHHE amp ND ND ND H h NH WNDNN HHHHE Enter RETURN for Equivalence 1 or enter number of alternate selection precede number of selection with R to reverse Enter X to stop downcoding at this stage gt 1 The second line in the display above gives the status of the enumeration Since no downcoding has yet been done the current and initial counts are identical 6 in each category Below the status line is a table of potential downcoding changes and their consequences e Allele Equivalence refers to the actual downcoding process that is making two alleles equivalent by changing the symbol of one to the symbol of another e Triple
312. llowed by the following display New File Creation Unlinked File 25 EXAMPLE Enter number of file group to which data file will belong gt 2 Here the Example Directory has been selected When a directory has been specified at this point ALTERDAT assumes that the file to be created will be linked to the Master File associated with the directory It is also assumed that an appropriate Code File has been created prior to running ALTERDAT In this case the following display appears Enter the name of the New Data File to start without extension gt TEST1 Enter the name of the Code File for TEST1 XMP or RETURN if T EST1 XMP a Multiple entry Data File Y N April 20 1999 ALTERDAT e 4 7 Since a linked Data File has been specified the file extension of the Master File here XMP is automatically provided although the name of this Data File may or may not have been added to DBFILES see program DBFILER in this Chapter Important the first entry in the Code File must be EGO Permanent ID with Standard Mnemonic EGO or ID A Standard Item List then appears and items may be chosen for entry with or without carry over etc in the same manner as in ADD mode Records may not be entered into a Linked Data File for individuals not yet in the Master File Starting a new Data File may be done only in Interactive Mode and the Delete function is not an option Command Q Qui
313. llowing commands MS DOS REN CODE TAB CODE lt EXT gt Unix mv code tab CODE lt EXT gt Macintosh Select the file name by clicking once on the name portion of the icon and replace code tab with CODE lt EXT gt Step 2 Run program ALTMASTR in START Mode choosing file extension lt EXT gt that is the same extension selected when renaming the Code File Enter data as required ALTMASTR generates an intermediate file named update lt EXT gt and creates a preliminary version of the Directory File DBFILES if the file does not already exist Step 3 Run program SETMASTR using extension lt EXT gt as the population identifier when prompted to do so SETMASTR creates the files required that is a Master File named MASTER lt EXT gt and a Master Pointer File MPOINT lt EXT gt SETMASTR also creates the Directory File DBFILES or modifies an existing copy to accommodate the new Master File Output file setmastr err may reveal inconsistencies that require correcting the original data see notes for ALTMASTR and SETMASTR in Chapter V Step 4 Run a spot check of records in MASTER lt EXT gt using program BROWSE or SHOW If data are not correct it may be necessary to edit records using program ALTMASTR and then run SETMASTR sa Creating a Master File from Imported Computer readable Data Creation of a Master File by importing computer readable data assumes that pedigree data are 4 2 Creating a Pedig
314. lly phenotypes and again to do the analysis Presence of a map file eliminates the need for the tallying step and can significantly speed execution If a Genotype Phenotype Map File is found and it contains the selected phenotype an alternate display appears 23 2 e INFER April 20 1999 ENOMAP XMP contains entries for ABO PHENO TYPE AUDR Enter RETURN to use GENOMAP XMP Otherwis nter name of alternate genotype phenotype map file loci not listed in a map file are assumed to be autosomal co dominant gt Next the format of inferred types is specified Normally inferred genotypes and phenotypes ar and incompletely known genotypes ar and a dash nclosed in parentheses represented by a single allele symbol Enter P to use parentheses and to display partial genotypes D to delete parentheses and partial genotypes from output Finally output file types are selected Full input records with appended inferred types plus INFERERR OUT Individuals with known prior and or inferred types plus INFERERR OUT Both output file types plus INFERERR OUT INFERERR OUT only Choose number corresponding to output format shown above gt a 2 A single locus chosen from the LOCUS Sub directory When the LOCUS Sub directory is selected choice 4 in the Introductory Display the following display showing all
315. loci for which types are to be inferred or C to continue gt Here three loci have been chosen INFER makes two initial assumptions about genetic loci First it assumes that the data are phenotypic unless one of the last three mnemonic words associated with the Code File entry for a locus is GENO or G TYPE in which case the data are interpreted as genotypic Second the program assumes that phenotypes are autosomal codominant and follow conventions listed in Appendix C Rules for Genotype and Phenotype Nomenclature unless specified otherwise in a Genotype Phenotype Map File GENOMAP lt EXT gt see Appendix A Definitions Data and File Types INFER first searches the Data Directory for map file GENOMAP lt EXT gt If the file is not found or if the selected phenotype is not included in it the following display appears o entries for selected loci found in GENOMAP XMP Enter RETURN if all loci are autosomal co dominant Otherwis nter name of alternate genotype phenotype map file loci not listed in a map file are assumed to be autosomal co dominant gt A Genotype Phenotype Map is not required for autosomal codominant loci that adhere to the conventions listed in Appendix C Nonetheless is it frequently helpful to generate a map for autosomal codominant loci using program GENOMAP because INFER will otherwise be forced to read through the entire Data File twice for each locus once to ta
316. locus which requires that sex be known for gene frequency calculations Enter P to select an appropriate pedigr fil Q to quit program 20 4 GENEFREQ April 20 1999 Notes e Important cautions GENEFREO calculations are approximate and should be used only for rough estimates of the overall genetic composition of the population included in a given file This is because a Calculations are made without regard to generational position or kinship relations between individuals b The program uses a simple counting procedure to calculate gene frequencies for codominant loci But for dominant recessive phenotypes the frequency of the recessive allele is estimated as Freq q VR where R is the frequency of the homozygous recessive phenotype in the population Frequencies of the dominant alleles are estimated as Freq p Di R VR where Di is the frequency of the ith homozygous dominant phenotype in the population These estimates depend on non zero frequencies of homozygous dominant phenotypes To guarantee this the count of homozygotes is changed from 0 to 1 when alleles are observed in heterozy gotes but are missing in their homozygous form in the population These estimates also depend on the assumption of random mating and large population size c Gene and genotype frequencies may be adjusted slightly so that they sum to 1 0 e A Phenotype Genotype Map need not be created for autosomal codominant loci that adher
317. lopment at many levels and provided numerous ideas for modification of the package as it has grown in scale Ms Denise Wahl assisted in the early stages of conversion to the Unix operating system Mr Tom Dyer continued this conversion and has been respon sible for the Unix systems interface including security of the package In the process he has made a number of important improvements to several of the programs Mr Richard Polich has contributed to programming and has been instrumental in implementing the Windows version of the package Mr Paul Mamelka has converted the programs for the Apple Macintosh developed the Mac interface that will serve as the prototype for subsequent graphic versions of PEDSYS and has taken the lead in organizing and restructuring source code into a modular form that facilitates implementation of the package on any hardware platform or operating system It has been a pleasure to work and learn from these individuals who make up the programming staff of the Population Genetics Laboratory The fact that we have found PEDSYS to serve our needs so successfully is not only the result of their technical skills but also of their ability to work with the scientists and technical staff of the Department of Genetics at the Southwest Foundation who have used the system and who continually make suggestions for its improvement D We have licensed an extremely efficient sorting routine Opt tech Sort for incorporation into
318. lt n gt 1 32 to set top row gt or lt lt n gt to shift window I lt n gt 1 6 to set window L to lock columns T to change instructions N for new file F to find H for help Q to quit gt April 20 1999 INFER e 23 11 Error Checking INFER identifies discrepancies between Ego and any one of Ego s parents When a discrepancy is found a record is written to file infererr out containing PIDs and genotypes including inferred types of EGO FA and MO and mnemonics of the locus Another type of error may occur when genotypes of parents are incompletely known and a there are more than 4 alleles represented in the offspring sibship or b there are too many combinations of alleles represented in the sibship given what is known about the parents and grandparents Here is an example of a display from program BROWSE showing contents of infererr out infererr out Top record 1 4 1 2 3 6 7 EGO FA MO E MO LOCUS G D063 ID038 ID042 B2 E E E ERROR EMO D068 ID062 ID047 B2 E E ERROR EMO D069 ID054 ID068 B2 E E ERROR EMO D071 ID045 ID034 D E E E ERROR EMO SandD Enter lt n gt or lt n gt for new page lt n gt 1 4 to set top row gt or lt lt n gt to shift window I lt n gt 1 8 to set window L to lock columns T to change instructions N for new file F to find H for help Q to quit gt Discrepancy codes It
319. lternative to renaming OUT files before rerunning a PEDSYS program Abbreviated pathnames of selected I O folders are listed in the Launch Window title bar while the folder names alone are shown in an application s title bar Changes to the I O path designations will not affect an active PEDSYS program it must be stopped and restarted for the new pathways to be used Setting Application Display Window Size The size of the display window opened by PEDSYS applications is controlled through the Set Display Size command on the Options menu of PedSys which opens a dialog titled Display Size when invoked Display Size Q Size application window to fill display monitor Specify window dimensions in characters Height O24 032 48 O64 080 Width 0980 O96 128 Q176 Q 240 M Confine zoomed window to primary monitor Window size may be set exactly using the predefined values or by entering them directly If Size to fill display monitor is selected the window is set to fill the monitor screen automatically when the application is launched The last option Confine zoomed window limits the growth of the display window when resized by clicking the zoom box If this option is unchecked the window will assume the designated display size which may be larger than the monitor depending on the dimensions and font size specified On a system with more than one monitor the zoomed d
320. lthough records be may selected for deletion while running in Interactive Mode final deletion is done as a batch process That is whenever deletion is specified a temporary Update File named lt filename gt DEL is created and used in turn as input to program DELRECS that must be run separately to incorporate these changes permanently into the Data File selected If the temporary Update File already exists the following sequence appears DEL already exists overwrite it Y N gt N Please rename QUANTGEN DEL before attempting to delete individuals from QUANTGEN XMP When an appropriate Update File is available the following sequence appears Last entry in QUANTGEN XMP is ID070 DELETE Record Enter individual s Permanent ID or RETURN to change mode of entry gt ID069 lt Ego ID and ID ID069 ELETE Record ADA Phenotype APOB Pvu2a Genotype Tot Ser Cholesterol 103 APOAI Level 99 2 Enter D to DELETE record or X to exit without deleting gt When all deletions have been entered ALTERDAT is ended with the Q command and program DELRECS is run to complete the process a The next three commands control settings for various editing features of ALTERDAT Command O Set order of access Entry of O at the command line toggles between random and sequential order of accessing items on records to be modified Al
321. lumn headings in the first record in translat tab Y N gt May 19 1999 TRANSLAT 45 1 The last option makes it possible to create a header record for output file translat tab a common format requirement for software that can read character delimited data 2 Delimited field to PEDSYS When delimited field to PEDSYS translation is chosen the following display appears Enter name of file to b gt examped tab Enter RETURN to create a converted to PEDSYS format Code File based on input data field widths or enter the name of an existing Code File to define the format of output records gt CODE XMP Here file examped tab containing character delimited records has been selected for conversion to PEDSYS format and rather than simply allowing input record field widths to establish PEDSYS item formats a pre existing Code File CODE XMP has been entered Item Descriptors in this Code File will be used to define the format of output records in translat out Note Use of a pre existing Code File in this manner will not work if any input field width is greater than the item field width defined in the Code File if Data Types conflict or if the number of input fields does not correspond with the number of items defined in the Code File Next the delimiter of fields in the input file is selected Convert examped tab to PI TAB character Comma EDSYS format Singl
322. ly 7 1999 DATES e 14 1 lt i gt lt n gt Y M D This sequence adds or subtracts constant lt n gt designated as year month or day by a following Y M or D respectively from item lt i gt containing a date Year may be expressed as integer plus a three digit fraction month as an integer plus a two digit fraction but day may be expressed as an integer only Combinations of year month and day are not permitted Example 13 6m yields the date at which each individual reaches six months of age lt i1 gt lt i2 gt Y M D This sequence adds or subtracts the contents of numerical item lt i2 gt designated as year month or day by a following Y M or D respectively from item lt i1 gt containing a date This feature is particularly useful when computing the date that an event occurs when only Ego s age at the time of the event is given Example suppose Ego s age in years at the birth of his or her first offspring is given in Item 22 of each Master File record The date of first birth could be determined by entering 13 22m C Entry of C produces the following display Operation 1 Select format of INPUT date representation for I Unit Format Interpretation Year YY YYY YYYY Number of integers 3 or 4 only Month MM MON MONTH Integer abbreviated and full alphabetic Day DD E Integer fraction of year days since 01 JAN Julian J lt base gt Days since base date 1 2 and 3 only i 1900 01 01 2 0
323. ly 8 1999 PEDTRIM e 32 5 Unacceptable values for CA1 Phenotype 1 EQ Unt 255 BO To ADD new values enter operator EQ NE GE GT LE or LT and value separated by a single blank in space below To DELETE value precede number from list above with D Enter C to continue gt eq lt As a consequence of these entries CA1 phenotypic values of Unt or blanks are defined as unaccep table when encountered on any record If these values are found missing data for either the APOB genotype or G6PD phenotype on same record will make Ego a candidate for removal from the pedigree Unacceptable values for CAl Phenotype 1 EQ Unt EQ EQ blanks To ADD new values enter operator EQ NE GE GT LE or LT and value separated by a single blank in space below To DELETE value precede number from list above with D Enter C to continue gt lt Unacceptable values are defined separately for each data item selected after which the next query appears Remove references to parents trimmed from pedigree Y N gt This instruction makes it possible to remove from EGO s record IDs of parents that have been trimmed from the pedigree When Standard Mnemonics are used in the input Code File PEDTRIM automatically replaces parental PIDs with blanks and sets their Sequential IDs to zero This is a requirement for many genetic analysis
324. m DPOINT lt EXT gt the Data Pointer File is rewritten when the Master File is updated lt filename gt lt EXT gt is an updated Data File from which records have been deleted More than one Data File may be updated lt filename gt OLD is a backup copy of a Data File as it was before deletions were made There may be backups of more than one Data File When deleting records from a Linked Data File Any Linked Data File from which records are to be deleted and its associated Code File lt filename gt DEL produced by program ALTERDAT containing IDs of records to be deleted from the Data File lt filename gt lt EXT gt is the updated Data File from which records have been deleted lt filename gt OLD is a backup copy of the Data File as it was before deletions were made lt filename gt ODE is a backup copy of lt filename gt DEL delrecs err contains a record and diagnosis of deletions that were attempted but were unsuc cessfully completed because of an error or inconsistency detected by the program DPOINT lt EXT gt the Data Pointer File is written when a Linked Data File is updated This will be a modified version of the previously created file Case 3 When deleting records from an unlinked Data File Input Output Any unlinked Data File from which records are to be deleted and its associated Code File lt filename gt DEL produced by program ALTERDAT containing PIDs of records to be deleted from the
325. m ITEMIZE using either the h human or n nonhuman Master File option that appears in an early screen display The principal function of ITEMIZE is to allow you to define and examine fields in an experimental fashion automatically creating a Code File itemize cde that defines the PEDSYS structure of a foreign file ITEMIZE can be run either with or without an input Code File If no input Code File is used you will be prompted for the field width data type and first mnemonic of each item In this case choose Standard Mnemonics when entering descriptors for EGO Father or Sire Mother or Dam Sex Birth Date and Exit Date when prompted If a Code File describing the structure of the foreign file is available it may used as input to ITEMIZE In this case Standard Mnemonics should have been used when entering descriptors for EGO Father or Sire Mother or Dam Sex Birth Date and Exit Date at the time the Code File was created In either case ITEMIZE checks to make sure that Standard Mnemonics required in a Master File EGO or ID BIRTH FA or SIRE MO or DAM and SEX appear in the output and that these items are given the appropriate Data Type and field width An opportunity to assign Standard Mnemonics is provided if they are not found initially after which the foreign file is copied with optional minor alterations into file itemize out Step 2 Run a spot check of records in translat out or itemize out using program BROWSE or S
326. m to run after setting the paths to Input Output folders Path Out Rename Delete Launch 0 d rt 3 June 10 1999 INSTALLATION and SETUP Macintosh OS F 5 Once a program has started PedSys reverts to background status It is brought to the foreground again when an application ends when a visible section of its Launch Window is clicked or when selec ted from the active application menu at the far right end of the menu bar PedSys may also be launched conveniently by creating an alias for the application file and moving it to the desktop for easy reference or by dragging the application icon to the Launcher window if it is active to create an alias there Instructions for running the individual applications may be found in the PEDSYS User Manual Fa 4 Setting Input Output Data Paths Before initiating an application a Data Folder should be selected using the Path In button Subsequently launched applications then will access this folder automatically The Path Out function is used to create or select an Output Folder to receive files created by PEDSYS applications If no separate folder is designated output files are sent to the input Data Folder by default There are no special restrictions on Output Folder location although it can be useful to keep it near or within the Data Folder Successively designated Output Folders can be used to store results from several analyses of the same file group as an a
327. mbered consecutively R lt n gt Display RECORD lt n gt RETURN Display next record ITEMIZE starts with a display of the first record in the input file selected However other records in the file may contain additional information such as non blank items that clarify the format Other records in the file may be displayed in one of two ways RETURN alone moves the display to the next record in sequence entry of R lt n gt displays the contents of record lt n gt where lt n gt is a number corresponding to a number in the range 1 through lt nrecs gt and lt nrecs gt is the number of records in the file All other screen characteristics ruler instruction and command lines etc remain unchanged X EXIT Entry of X causes the program to write output in files itemize out and itemize cde If any items have been assigned the mnemonic SKIP however the following instruction is displayed before files are saved 24 6 e ITEMIZE April 20 1999 EXCLUDE all skipped fields xclude skipped fields only if BLANK in all records INCLUDE skipped fields QUIT program without saving output Usually skipped fields are not wanted in program output option E However their inclusion option I is sometimes useful because an unreduced itemize cde can be used as a Code File for the original input Data File It is frequently desirable to skip fields that are blank on every record of the input file Unless every
328. me gt OLD 2 A 12 9 The Directory File DBFILES 22 A 12 10 The Shell Menu File PEDMENU A 15 11 The Device Control File DEVICES 2 A 15 12 The Standard Mnemonics File CODE STD A 18 13 The Genotype Phenotype Mapping File GENOMAP lt EXT gt A 19 14 Temporary System Files A 20 15 The Data Path File PATHWAY 0 c ccc eee ene A 21 APPENDIX B Program TRANSLAT Record Format Translations TBA APPENDIX C Rules for Genotype and Phenotype Nomenclature TBA APPENDIX D nenscript seras etes ae tale PL illa TBA APPENDIX E INSTALLATION and SETUP Sun Microsystems Unix Solaris 2 5 E 1 APPENDIX F INSTALLATION and SETUP Apple Macintosh OS F 1 APPENDIX G INSTALLATION and SETUP Windows TBA INDEX 25 p DALLA iaia LIA TBA Fi iv June 12 1999 Acknowledgments The concepts underlying PEDSYS were originally developed in 1978 79 while I was on the faculty at the Pennsylvania State University During that time I devised a version of the PEDSYS record format and wrote four of the original Data Management Programs INDEX LIST SO
329. ment of both parental PIDs is found to be incorrect and ALTMASTR is used to delete these PIDs from EGO s record If SETMASTR finds no inconsistencies in the family as it is determined from the DAM s perspective EGO s DAM PID will be erased and the number of the DAM s offspring NKIDS will be reduced by one If however there is an error in the family from the SIRE s perspective EGO is not listed among SIRE s offspring for instance SETMASTR will not remove EGO s SIRE PID nor will it reduce the SIRE s NKIDS by one Unless proper steps are taken the resulting inconsistent tabulation of NKIDS for the two parents can persist in the Master File even after subsequent runs of ALTMASTR and SETMASTR What must be done when errors 51 74 are reported is to run program INDEX at some point after corrections are made with ALTMASTR and SETMASTR INDEX will re compute NKIDS and re establish all family links Group 5 Conflict in Gender Assignment SETMASTR will not allow change of SEX assignment for EGO already present in the Master File if a EGO is listed as a parent in other Master File records or b the record of the individual listed as EGO s first offspring does not in turn list EGO as a parent If these conditions are found by cross checking PIDs of family members in the Master File the following errors may be reported lt ego gt SEX not changed EGO listed as lt parntyp gt of KID1 lt kidl gt in MF lt ego gt SEX not changed EGO no
330. missions for Sun Microsystems Solaris 2 5 compatible with later versions of this operating system 1 Directory Organization The basic scheme assigns executable program files to an independent Program Directory which is kept separate from any number of Data Directories which in turn may contain one or more sub directories These directories are set at the same hierarchical level below a PEDSYS root directory as shown in the following diagram PEDSYS Root Directory A a PEDSYS PEDSYS PEDSYS Program Directory Data Directory Data Directory 4 y Y DN Sub directory Sub directory Sub directory Sub directory a The PEDSYS root directory Typical contents of the Unix PEDSYS root directory are as follows example menu where CODE STD and DEVICES are the Standard Mnemonics File and Device Control File respectively see Appendix A DBDIRECT is a file used as input to program setpath containing a list of pathways to the various Data Directories see Chapter III bin is the name of the Program Directory and menu is the name of a directory containing text files used for display of program functions and file access The only Data Directory shown is example which reflects the state of the root directory at June 10 1999 INSTALLATION and SETUP SOLARIS 2 5 E 1 the time of its installation b The PEDSYS Program Directory bin Files typical of the Program Directory are shown in the display below this lis
331. mming but note that what was originally a single pedigree has been broken into two represented by hatched and stippled fill patterns respectively plus two individuals remaining in the sample but now showing no family links at all black fill ID038 r I I I I I I I I I I ID015 A IDO71 AB A Pedigree Draw The reasons for removal of the six individuals shown are as follows ID049 lacks data for both CA1 and G6PD phenotypes and has no offspring ID069 lacks data for both APOB genotype and CA1 phenotype and has no offspring ID067 has data only for CA1 phenotype and has no offspring July 8 1999 PEDTRIM e 32 7 ID068 and ID015 are missing APOB genotypes and ADA and CA1 phenotypes and they are left without offspring in the pedigree since ID067 and ID069 have been trimmed ID062 is left without offspring in the pedigree since ID015 and ID068 have been trimmed Note that as the result of removing the six individuals the original pedigree has been broken into four separate subunits each represented in the diagram by distinctive shading Individuals ID019 and ID062 represented by a black symbol are no longer connected to any pedigree but remain in the output file because they has valid data which may be useful in population measures such as gene and genotype frequencies etc e File pedtrim tab contains the table of critical data items that determine the inclusion of individuals in the trimmed pedigree
332. must be selected by entering a pointer that is an integer designating the position of the record in the file e Sometimes the predefined order implicit in PEDSYS file linkage is not desirable One way to overcome this order is to treat a linked Data File as an unlinked file which forces PEDSYS programs to ignore relationships between records defined in the Master Pointer File the Data Pointer File and the internal pointers in any Multiple entry Data File This can be accomplished by selecting the Unlinked category in the initial File List Display and typing in the file name rather than selecting the file from the numbered list e The Find function relies on a simple sequential search through the records in a file and is consequently quite slow particularly when searching for substrings Searches for values known to occur in multiple records such as is the case with Multiple entry Data Files are often better done with program SUBSET e Alternates are provided for the leading command characters specifying Sequential ID Numbers This is because there is the possibility of conflict between the default and PIDs that may begin with the same characters For example suppose a Master File contains records of individuals identified by PIDs all or some of which begin with the letter S followed directly by a number S10 S11 S12 etc In this case there is no way to distinguish between entry of the PID S10 and the Sequential ID Number 10 which mus
333. n index to Ego s mate Indexing a single individual requires an Input File containing the Permanent ID of Ego and of the individual to be indexed if other than Ego Notes on Input Record Format T If the input Code File contains parental mnemonics FA and MO the population is assumed to be human If the Code File contains mnemonics SIRE and DAM the population is assumed to be nonhuman e Choice 1 INDEX requires an input Data File with records containing items specified by the table below to index of EGO FA and MO and produce Master File Order of input Code File entries is not fixed and will depend on the order of the data in the Input File Required entries may be interspersed with entries describing other items in data records Mnemonic codes for required entries must be used exactly as shown see description of the Standard Mnemonics File in Appendix A INDEX will terminate with an error message if any of the required items are missing from the input Code File Exit Date and Exit Code are optional items for all PEDSYS programs but may be required for some demographic analyses see Notes on Master File Record Format in Appendix A April 19 1999 INDEX e 22 5 Item name nemonic Type Ego Permanent ID Father s Permanent ID other s Permanent ID Sex EX Birth Date Yr Mo Da BIR Exit Date Yr Mo Da EXIT Exit Code EXCODE Code File may contain additional items PEDSYS date format eight di
334. n phenotypes and genotypes shown above E switches to Edit Mode A starts the beginning sequence for entry of a new locus D is followed by a request for the locus to be deleted C begins execution of the program See Section 2 below Editing a previously created Genotype Phenotype Map File for more details on Edit commands Option M Manual creation of map table locus data read from file If option M is chosen the following display appears in which phenotype symbols are entered Enter symbols for PH ES in any order ETURN alone when done gt A gt B gt C gt AB gt AC Are these correct Y N gt y Next correspondences between phenotypes entered above and the possible genotypic combina tions derived from them must be established also manually Note that locus mnemonics are dis played since data for the ADA locus has been read from a file Locus ADA PH F Mode of inheritance AUCD Phenotypes 1A 2 B Genotypes 1 A A A 3 A B 5 B C 2 A C AC 4 C C 6 B B Enter number corresponding to GENOTYPE to be assigned to a phenotype Enter AP to add DP to delete a phenotype AA to add DA to delete or RA to replace allele symbol Enter M to change locus mnemonics I to change mode of inheritance C to continue gt 4 Enter number of PHENOTYPE for A C gt 3 In the display above correspondence betwee
335. n selected initiates the find function see below Writes EGO s entire current record in standard PEDSYS record format to output file show lt n gt out Code File show lt n gt cde where lt n gt is the order in which alternate files are written For example if the first record to be written is the Marker Phenotype entry for individual ID061 shown in the screen above the entire record will be saved in file show1 out If the next write command is issued while displaying the Master File entry for this individual the first screen display shown above that entire Master File record will be saved in file show2 out Parental records are not written When SHOW is used with an unlinked file the single record displayed on the screen is written to file show1 out This command results in a return to the File List from which a new file or set of files may be selected for display in the usual manner Entry of an H produces the following help display April 19 1999 SHOW e 40 3 To display a record enter a Permanent ID S followed by EGO Sequential ID or followed by a number representing a record s position in the file and then hit RETURN To move FORWARD through a file enter RETURN for steps of one precede RETURN with lt n gt for steps of lt n gt To move BACKWARD through file precede RETURN with for steps of one lt n gt for steps of lt n gt To change the order of items or limit display to
336. n the first three genotypes listed A A A C and A B and their respective phenotypes A AC and AB have been entered while matching of geno type 4 C C with phenotype 3 C has been specified This is essentially the same display as is used for Edit Mode shown below 21 4 e GENOMAP June 10 1999 When this process is finished the program reverts to the same sequence of operations as shown above for option A automatic creation of the map table confirmation display etc a Choice K Genotype Phenotype Map Data Entered from Keyboard no data read from file When choice K is selected all data must be entered manually First to be entered are locus mne monics Although not illustrated here autosomal dominant recessive AUDR mode of inheritance has been selected for the following example Enter one or more mnemonics for the locus NOTE These should be identical to mnemonics found in the Code File of the corresponding Data File alone to continue to next step gt ABO Enter mnemonic Enter mnemonic Enter mnemonic Enter mnemonic Enter RETURN Here mnemonics for the ABO phenotype have been entered Next allele symbols are entered followed by phenotype symbols Note that all symbols are case sensitive and that alleles and pheno types need not have the same case gt a gt b gt O gt Are these correct Y N gt y
337. n the same item on all the other records associated with that individual This feature makes it unnecessary to make the same change to the same item in each of a series of multiple records for the same individual 1 Sample Number 4 Sample Status 7 Comments 2 Date Taken 5 Animal Status 3 Vial T 6 Project Code ALTERDAT Items to be modified File SAMPLES XMP Enter numbers corresponding to items to be modified Precede number with H to carry over entry of item from one record to the next Enter A or HA to include all items D to duplicate change of same item in all of EGO s records C to continue gt April 20 1999 ALTERDAT e 4 9 The Duplicate and Hold over functions may be used simultaneously although the combined effect can be confusing making it imperative to check that records are configured properly before beginning a long ALTERDAT session in which many records are entered or modified This is particularly important when running in Interactive Mode where records are changed directly without an intervening step Choice of items to be edited is followed by a request for a PID after which follows an Edit display ID069 Record 3 3 EDIT Mode Random Order Sample Number Date Vial Taken Type Sample Status Animal Status gt W250 lt gt 19980414 lt gt TYG lt gt lt gt lt Project Code Comments through e
338. nals are limited to EQ equal to and NE not equal Compound searches for occurrences of combined item values are not possible a 40 8 SHOW April 19 1999 SHOWDATA Program SHOWDATA gives a direct screen display of all records for a single individual from a PEDSYS Multiple entry Data File Single records for this individual in the Master File and linked Single entry Data Files may be displayed as well SHOWDATA is in some ways similar to BROWSE but unlike BROWSE it is individual oriented rather than record oriented That is SHOWDATA displays multiple records of a single individual whereas BROWSE displays multiple records for more than one individual in a file Introductory Display PEDSYS program SHOWDATA Copyright 1992 1999 SFBR SHOWDATA gives a direct screen display of all records for a single individual Unlinked File Ps EXAI PLE De LOCUS Sub directory Enter number file name or Q to quit gt Access to records in Linked Data Files may follow either 1 the order of corresponding records in the Master File or 2 the order of records in the Data File itself Records in unlinked files on the other hand are sorted and temporarily indexed by SHOWDATA making order of access a function only of their file position These considerations lead to slightly different effects of some of the program s com mands dependent upon the file type which will be noted in the command description
339. nction selected from the keyboard PEDSYSP EXE calls the appropriate PEDSYS program c Macintosh OS PEDSYS program names are kept in a file named PEDSYS RSRC on the Macintosh These names are displayed in the program shell menu and are also used to call the appropriate PEDSYS program Although any of these files may be modified with the appropriate editor there should be no need to do so 11 The Device Control File To assure that PEDSYS listings are properly formatted PEDSYS programs LIST REPORT and TALLY control printer characteristics such as line length and character size with codes read from a June 12 1999 APPENDIX A e A 15 Device Control File named DEVICES located in the PEDSYS Program Directory Codes are specified by the manufacturer of the printer Here is an example of DEVICES configured for the Epson 286e printer attached to an MS DOS computer Letters in parentheses on the right hand side of the figure refer to notes that follow and do not actually appear in the file 2 Number of devices PRN 4 Epson 286e 136 050 lt 018 gt lt 027 gt Pp 163 050 lt 018 gt lt 027 gt M 233 050 lt 015 gt lt 027 gt Pp 272 050 lt 015 gt lt 027 gt M lt 012 gt lt 027 gt CON 1 Console screen 080 024 lt 000 gt lt 000 gt a b c c c c d b c c Notes a The first record in file DEVICES I2 format specifies the number of output devices to which pro gram LIST may
340. nd at the same time to be able to combine these data a with a common pool of demographic and genealogical information about the population and b with data sets collected in other projects To accommodate this requirement PEDSYS databases are organized around a Master File containing basic information on vital events and genealogical relationships for individuals in the population Any number of independently developed Data Files may be joined as needed to the appropriate Master File Data Files can be copied or combined in various ways to form entirely new files that maintain their linkage with the Master File 2 Another critical need was the ability to import foreign data that is files developed on other database systems and to export PEDSYS data to other programs or computers for analysis This requirement was met by choosing a simple file structure based on formatted records containing nothing but data represented by printable ASCII characters That is there are no file headers record descriptors or control characters that must be processed or avoided before accessing information kept in the database In addition several of the PEDSYS General Data Management programs are designed to transform or reconfigure ASCII data into any required format with considerable ease and flexibility 3 Although we anticipated that some individuals would become highly skilled in the use of the system we felt that it was important for non experts to be abl
341. nd for autosomal loci exhibiting dominance It is optional for autosomal codominant phenotypes whose nomenclature adheres to PEDSYS conventions listed below This file is used by programs GENCHECK GENEFREO and INFER and is normally created with program GENOMAP An example showing entries for the ABO blood group is given below Records in this file are formatted as follows Record 1 Locus Descriptor Record a c da e f 0000000000000 000 29 33 37 AT June 12 1999 APPENDIX A A 19 Records 4 5 Phenotype Label Records i Key j Map 0000000000000 Start 14 Format 13X lt np gt A1 Records 6 lt nc gt Genotype Phenotype Mapping Record k Format 2 A5 1x lt np gt A1 Where represents a character in a field read by PEDSYS programs o represents a single blank ignored by PEDSYS programs often used as a visual separator is a visual marker pointing to the first character in each field also appears between single quotes as a data constant in records 4 and higher Numbers below the vertical markers in the diagrams above represent the starting column of each field e Notes on GENOMAP lt ext gt Record Formats a A Locus Descriptor Record is always the first record in the group of records defining the relationships of phenotypes and genotypes for a given locus Length of this record is fixed at 41 characters b The first f
342. ned in the file PSManual pds It may be viewed or printed with Acrobat Reader 2 1 3 0 Restrictions Once installed the PedSys folder may be placed at any level in a hard drive s folder hierarchy subject to two restrictions e The fully qualified pathname of the folder PedSys formed by joining parent folder names in the form folder1 folder2 folder3 must be under 244 characters in length This pathname length re striction applies to the location of Data Folders as well e The fully qualified pathname of a folder or file accessed by the system must contain no spaces or Mac only characters This restriction is required by the standard sort routine used by many PEDSYS applications which was designed with Unix conventions in mind Limiting folder names to print able ASCII characters e g 0 9 A Z a z period dash and underscore is recommended Enabling Custom Icons PEDSYS for Macintosh features its own set of customized icons identifying applications and support files which come with the system or are created by it The same icon is used for all applications except PedSys Double clicking any of the document icons causes PedSys to be launched F 4 INSTALLATION and SETUP Solaris 2 5 June 10 1999 Application amp Support File Icons 7 items 624K in disk 9 5 MB available i eA A K a al d dd dl Age CODE STD DEVICES LASTPATH PATHWAY PedSys PedSys settings If PEDSYS s customized icons do not appear when
343. ner analogous to the column locking feature of program BROWSE permitting reordering of items displayed and making it possible to assure that selected items of interest always appear on the first screen page See explanation of row locking below If the complete record will not fit on a single page entry of P lt n gt where lt n gt is a number from 1 through the total number of pages displays the corresponding page Entry of P alone advances the screen page by one This command makes it possible to switch the SHOW display rapidly between linked files Initial entry of an asterisk has one of two consequences depending on the prior state of the program If multiple files have been selected previously from the Secondary File List the record display switches to the next file selected If multiple files have not yet been chosen a File Selection display appears from which one or more linked Data Files may be selected Subsequently after returning to the record display entry of an asterisk switches the display to one of the selected files The top record of each of these displays will belong to the same individual providing that there is in fact an entry for that individual in the newly selected file If there is no entry in the file the message No record for lt PID gt in lt filename gt Enter RETURN for the first record of this file or for next file This option applies only when a Master File or linked Data File has bee
344. nerate a new lt filename gt DEL by selecting records for deletion in the current Data File using program ALTERDAT before running DELRECS again Fa Notes e If both additions and deletions have been made to a Master File that is if ALTMASTR has pro duced both UPDATE lt EXT gt and DELETE lt EXT gt both SETMASTR and DELRECS must be run to complete the update process SETMASTR should be run before running DELRECS e If both additions and deletions have been made to a Data File that is if ALTERDAT has produced both lt filename gt UPD and lt filename gt DEL both SETDATA and DELRECS must be run to com plete the update process SETDATA should be run before running DELRECS Pi Files Case 1 When deleting records from a Master File Input Any Master File and its associated Code File Any linked Data Files from which records must be deleted in parallel with deletions from the Master File DELETE lt EXT gt produced by program ALTMASTR containing PIDs of individuals to be del eted from the Master File Output MASTER lt EXT gt is the updated Master File produced by the program MASTER OLD is a backup copy of the input Master File 16 2 e DELRECS April 20 1999 Case 2 Input Output DELETE OLD is a backup copy of DELETE lt EXT gt delrecs err contains a record and diagnosis of deletions that were attempted but were unsuc cessfully completed because of an error or inconsistency detected by the progra
345. ng the population for which the Master File is to be created The following instruction appears on the screen if START Mode is selected April 20 1999 ALTMASTR e 5 3 File UPDATE lt ext gt will be produced and used to create a new MASTER lt ext gt where lt ext gt is a three character file extension used as a population iden tifier Enter the identifier for this population If a Code File with the extension entered here does not exist the following error message appears ERROR CODE DOG does not exist Create an appropriately named Master Cod File or if one exists use the correct identifier or Q to quit program gt mn ter RETURN to continue If a Master File with the same extension already exists the following message appears ERROR MASTER XMP already exists Delete or rename this file or use another identifier Press RETURN to continue or Q to quit program gt A Standard Item List is used and items may be chosen for entry with or without carry over in the same manner as in CHANGE Mode see above The following display appears upon exiting the program after all changes are made KEKE KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK AAA AA AAA AA AA AAA AAA To complete the process of changing MASTE ETMASTR it will be necessary to run program S R lt ext gt KKKAKAKKAAAKAKAKAAKKAAKAK
346. noting mode of inheritance AUCD Record 2 contains symbols for each of the alleles Record 3 is blank Records 4 5 contain phenotype labels Records 6 11 contain genotype symbols and markers designating phenotypes they express This pattern is repeated for the ABO G6PD and Y linked loci that follow A more detailed de scription of formats of the records in this file can be found in Appendix A Files Input Console and or a Data File containing phenotypic or genotypic data and optionally a previously constructed Genotype Phenotype Map File Output File genomap tab Program limits Tables for up to 50 loci each with up to 13 alleles may be constructed Fe June 10 1999 GENOMAP e 21 13 21 14 GENOMAP June 10 1999 INDEX The chief function of program INDEX is to create a PEDSYS Master File by assigning a Sequential ID number pointer to selected individuals in a pedigree file and arranging data items in a prede termined order on each record Other functions are to compute numbers of individuals offspring and to create a Master Pointer File see Appendix A File Types Introductory Display EDSYS program INDEX Copyright 1992 1999 SFBR INDEX assigns a Sequential ID number file pointer to individuals in a file Individuals may be indexed as follows EGO FA and MO adding pointers to offspring sibs etc Same as above plus another individual such as a mate EGO FA and MO
347. notypes 1 A 2 AB Genotypes 1 A A A 3 A C AC 5 B C BC 2 A B AB 4 B B B 6 C C C Enter number corresponding to GENOTYPE to be assigned to a phenotype Enter AP to add DP to delete a phenotype AA to add DA to delete or RA to replace allele symbol Enter M to change locus mnemonics I to change mode of inheritance C to continue gt Edit Options Genotype phenotype assignment change Assignment of a genotype to a particular phenotype may be changed by entering a number corresponding to the genotype which produces a request for the number of s corresponding phenotype Enter number corresponding to GENOTYPE to be assigned to a phenotype Enter AP to add DP to delete a phenotype AA to add DA to delete or RA to replace allele symbol Enter M to change locus mnemonics I to change mode of inheritance C to continue gt 2 Enter number of PHENOTYPE for A C gt 1 Here genotype 2 symbols A B will be reassigned phenotype 1 symbol A Note that such a change would require substantial further alterations to the table if it were to made permanent see option AA below AP When the AP Add phenotype option is entered in the Edit Menu the following display appears requesting entry of a symbol for the new phenotype Enter new phenotype symbol gt D Here symbol D has been entered This symbol is adde
348. notypes on an a priori basis as illustrated in the diagram below ID015 Pedigree DrAw Directly below each individual s PID is shown the ADA phenotype exactly as it appears in the ADA locus file Note that there is no entry for individuals ID015 ID045 ID056 ID067 or ID068 Be April 20 1999 INFER e 23 5 low each phenotype is an a priori genotype assignment since the locus is codominant genotypes can be deduced directly from phenotypes Note also that alleles and phenotypes are represented by identical symbols here upper case which illustrates the convention followed when a Phenotype Genotype Map is not used INFER starts with this information and iteratively attempts to fill in the missing types according to the Mendelian laws The results can be seen in the next diagram ID067 BC BC Pedigree DrAw Here inferred allele types genotypes and or phenotypes are surrounded by parentheses Inferences have been made from both parents and offspring Since we know a priori that parents ID062 and ID047 are both BB homozygotes we infer that their offspring ID068 and ID015 must share the same genotype and phenotype assuming correct assignment of paternity In contrast we know a priori that offspring ID071 has received an A an allele from each parent and that ID049 has inherited a pair of B alleles from the same parents Their mother ID034 is known to have phenotype AB and so we infer that father ID045 is also phenotype AB of
349. nt ID Sex M F or U Exit Date YYYYMMDD Exit Code ENE Ego ID Tot APOAI Ser RATION NU ADA Phenotype APOB Pvu2a Geno type Cholestero Level U a EPDRAW Pale tte 4 Miscellaneous r IF gt enter lt I DX Last IF gt IF gt 12 Dot centered E Dot lower left Dot lower rght F G Centered entry IF 23 D temNo gt lt Operator gt lt Test gt THEN SYMBOL EQ AB THEN S Enter H for explanation and shortcuts centered X above Inserted T H Heavy symbol EQ BLANKS AND 24 lt symbol gt IF gt 10 NE b AND C to continue I upper right J upper right M Gray fill K Circle up rt O Horiz L Bar above EQ BLANKS THEN SYMBOL EXAMPLE 10 LT k942131 THEN SYMBOL N Vert hatch hatch P Diag hatch Here the symbol representing any individual with a missing ADA Phenotype Item 23 will be filled with gray shading 34 6 PREPDRAW May 4 1999 Note A total of no more than four symbol types may be assigned to the same individual from Palette 1 and Palette 4 combined Additional attributes may be assigned to a single individual from other palettes for a total of six altogether Step 4 Modifying the Symbol Selection Table When selection of symbol types and attributes is done the palette selection display appears with an additional choice providing
350. nteger surrounded by angle brackets lt gt The actual content of the control string is specified by the manu facturer of the printer A single blank must be left between elements Format of these records is 2 13 1X A72 In this example the first control record specifies a 136 character line the maximum number of pica font characters that will fit on standard 14 inch computer paper and a limit of 50 records per page Although it may be desirable at times to fit a few more lines on a standard page we have found the 50 record limit to be convenient Next follows ASCII character 18 DC2 or CTRL R which is the Epson control code for standard uncompressed print and then the sequence ASCII character 27 ESC and the letter P which together specify the Pica font The fourth control record specifies a line length of 272 characters a page length of 50 ASCII character 15 SI or CTRL O which sets compressed print and the sequence ESC M which specifies the elite font etc Line length 80 and 24 records are specified for device CON but ASCII character 0 signifies that no font control is required Note The console screen should be the last device listed in DEVICES A 16 e APPENDIX A June 12 1999 d The record following the last control record for a given device contains control codes that LIST sends to the printer after a PEDSYS listing is finished This sequence resets the printer to the configura tion it had before LIST was used Rules for com
351. nter 110 60 lt 000 gt CON 1 Console 0 0 lt 000 gt lt 000 gt File DEVICES must be present in the PEDSYS Program Directory see Chapter II SETUP and INSTALLATION The file should be created with any text editor at the time PEDSYS is installed The Standard Mnemonics File A permanent input file containing standardized mnemonics and field lengths named CODE STD must be present in the PEDSYS Program Directory The first two columns of this file contain invariant mnemonics appropriate for non human animal and human pedigrees respectively The last two columns contain the lower and upper range of field lengths of required Master File items respectively The contents of this file which is shown below should not be altered in any way SEQ SEQ SSEQ FSEQ DSEQ SEQ KID1 KID1 PSIB PSIB SIB SIB FSIB FSIB NKID NKID PSIBSZ PSIBSZ SIBSZ SIBSZ FSIBSZ FSIBSZ ID EGO BIRTH BIR SIRE FA DAM O w CG F a a A CO O1 O1 O1 O1 O1 O1 uo NN N CO OC O1 O1 O1 oOo oo wW w A 18 e APPENDIX A June 12 1999 CODE STD is required input for programs ALTERDAT BROWSE ALTMASTR COUNTPED DATES DELRECS EXCLUDE INDEX MERGE NUCFAM REPORT SETMASTR SHOW SHOWDATA SIBSHIP and VERIFIER 13 The Genotype Phenotype Mapping File Relationships between genotypes and the phenotypes they express are defined in a file named GENOMAP lt ext gt This mapping is required for X linked loci a
352. nter C to continue gt In this example Item 3 the CA1 Phenotype has been selected Entry of C produces the following display in which unacceptable values for this item may be added Unacceptable values for CAl Phenotype To ADD new values enter operator EQ NE GE GT LE or LT and value separated by a single blank in space below Enter C to continue gt eq Unt Here eq Unt appearing in the entry space indicates that Unt will be designated an unacceptable value for the CA1 phenotype As each value added it is numbered and displayed at the top of the screen where it can be modified with the editing function provided Unacceptable values for CAl Phenotype EQ Unt To ADD new values enter operator EQ NE GE GT LE or LT and value separated by a single blank in space below To DELETE value precede number from list above with D Enter C to continue gt eq lt As can be seen in this display value Unt has become a numbered value which can be edited according to instructions at the bottom of the screen while the entry space contains the string eq indicating that will be added to the list of invalid data entries Note Having chosen to override the default exclusion criterion missing data must be defined explicit ly This is done by specifying blank fields as unacceptable values as shown in the following screen display Ju
353. ntical to one of the PIDs found in the Master File Creation and linkage of a Data File requires is done in four steps Step 1 Create a Code File for the new PEDSYS Data File by running program CODE choosing Create Mode and skipping the Master Code File options CODE will request entry of optional labels mnemonics field lengths and data types When entry is finished the output file should be named lt filename gt CDE where lt filename gt is the name chosen to identify the new Data File If you forget and give the file its default name of code tab it will be necessary to rename it Depending on the computer on which PEDSYS is installed this can be done with one of the following commands MS DOS REN CODE TAB lt FILENAME gt CDE Unix mv code tab lt FILENAME gt CDE Macintosh Select the file name by clicking once on the name portion of the icon and replace code tab with lt FILENAME gt CDE Step 2 Run program ALTERDAT in START Mode entering the name of the new Data File and the Master File to which it will be linked when prompted These should be lt FILENAME gt lt EXT gt and lt FILENAME gt CDE respectively that is the same file name selected when renaming the Code File in Step 1 above ALTERDAT will modify the Code File as needed by adding an internal pointer mnemonic PNTR as the last field if the file is a Multiple entry Data File Enter data as required in ADD Mode ALTERDAT creates a Data
354. ntries or X to gt HLM lt gt Enter number of item to be modified EXIT without saving changes for current record ew map lt ow 4 lt n gt to SAVE to advance gt This display is slightly different from that associated with the Single entry file The most recent ly entered record is displayed initially Record 3 of 3 in the example above The earlier records for this individual are accessed by entering a minus sign If an earlier record is currently being shown on the screen entry of will display the next most recent record Entry of lt n gt or lt n gt will result in the display the of record lt n gt steps prior or subsequent respectively to the currently displayed record Command A Add records to a Linked Multiple entry Data File The ADD procedure for Linked Multiple entry files is similar to that for Linked Single entry files except that in this case ALTERDAT permits addition of records with IDs that duplicate those already in the file and the Duplicate feature is not provided Command D Delete records from a Linked Multiple entry Data File The delete procedure for Multiple entry files is similar to that for Single entry files except that provision is made to delete all of Ego s multiple records with a single command the DA command Record 3 3 ID ID069 Animal ID Sample Number Date Vial Taken Type Sample Status Animal Statu
355. o OE ee RU hob fe eNOS ia dai 44 1 TRANSLAT An ie hat al a LE ed rar ed ne nb 45 1 TRIPLETS aie er ee ee AN cieli 46 1 YEBRIFIER sud dle eee de IRR tia Anna 47 1 APPENDIX A Definitions Data and File Types A 1 As Definitions ersen pde rreran pali ne Tan EE ERE eee Se mena ae A 3 Bi Data Types is ir ee ne TR baila ent ess eve A 3 Cy File Types en des dti Panne ten en tae battled area damien sans A 4 1 Program Files lt progname gt EXE A 4 2 The Master File MASTER lt EXT gt A 4 3 Data Files lt filename gt lt EXT gt 22 A 6 a UNG Le Entry circeo tai illa rap aa A 6 b Multiple Entiy ela O AL AA nale A 7 4 Code Files CODE lt EXT gt lt filename gt CDE LL A 7 5 The Master Pointer File MPOINT lt EXT gt Li A 9 6 The Data Pointer File DPOINT lt EXT gt LL A 10 7 Reusable Output Files eee nee A 10 a Data Output Files lt filename gt out A 10 b Error Files lt filename gt err A 11 c Log Files lt filename gt log A 11 d Tabular Output Files lt filename gt tab A 11 e Miscellaneous Output Files ee A 11 8 Backup Files lt filena
356. o quit program Press RETURN to continue gt Q exits the program 2 Displaying Unlinked Data Files Enter P to see the next or P lt n gt to see the lt n gt th page of multiple Enter to switch cyclically from one file to the next If files have not been preselected initial entry of presents a File List from which When an unlinked file is selected for display the following display appears from which an identi fier common to multiple records usually a PID is selected 1 Animal ID 4 Vial Type 7 Project Code 2 Sample Number 5 Sample Status 8 Comments 3 Date Taken 6 Animal Status 9 INTERNAL POINT SHOWDATA Select ID and sort items File reformat out Enter additional item numbers as needed to order records within sets Enter item number corresponding to common identifier of multiple records By default records are sorted in ascending order precede item numbers with a D to sort in descending order Enter C to continue gt 1 Once an identifier has been selected a screen display identical in configuration to those shown for Linked Files appears Commands Control of unlinked file display is for the most part the same as for Linked Files with the following differences April 19 1999 SHOWDATA e 41 5 S lt n gt In the case of unlinked files lt n gt is interpreted as the nth individual in the Data File rather than as a Sequential ID Number of
357. of the Edit Menu Here again such a change would require further alterations to the table if it were to made per manent see option DP above RA When the RA Replace allele option is entered the following display appears requesting entry first of a symbol to be replaced in the list and then its replacement Enter allele symbol to be replaced gt A Enter new allele symbol gt a This would result in substituting a lower case a for all occurrences of upper case A in the list of genotypes shown in the bottom half of the Edit Menu Care must be taken that such replacements actually reflect the form and content of symbols in the locus file to which the Genotype Phenotype Map Table applies M Entry of M Change locus mnemonics produces the following display Enter one or more mnemonics for the locus NOTE These should be identical to mnemonics found in the Code File of the corresponding Data File Enter ETURN alone to continue to next step Enter mnemonic 1 Enter mnemonic 2 Enter mnemonic Here the mnemonics ADA PHENO TYPE are changed to ADA P TYPE This change will be reflected in the first line of the map table for the locus in question I The I option Change mode of inheritance produces the following display 21 10 e GENOMAP June 10 1999 Locus ADA P TYPE Mode of inheritance AUCD Autosomal codominant Autosomal dominant recessive X linke
358. offspring or b no parents and a single offspring even though this offspring may have data The file containing the pedigree may be either a Master File or a pedigree file consisting minimally of records containing IDs for Ego and Ego s parents Data upon which trimming is based may be included on records in the pedigree file or may be taken from one or more Data Files if they can be matched with records in the pedigree file Introductory Display EDSYS program PEDTRIM Copyright 1992 1999 SFBR PEDTRIM iteratively removes from a pedigree all individuals whose phenotypic or genotypic data are missing if they have a no offspring or b no parents and single offspring 1 Unlinked File EXAMPLE 3 LOCUS Sub directory Enter number file name or Q to quit gt 2 1 Selecting Data Files a A Linked Data file containing genotypic or phenotypic data Linked Files Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Data may be selected from one or more linked files Enter numbers corres ponding to files s above Enter RETURN alone to continue to next step gt 2 Here the Markers Quantitative Phenotypes file has been selected from which items are selected for inclusion in output records 1 EGO Permanent ID 3 ADA Phenotype 5 CA1 Phenotype 2 ABO Phenotype 4 APOB Pvu2a Genotype 6 G6F Phenotype PEDTRIM Selec
359. on the relationship fry 0 5 fxs fxD where fxy is the coefficient of kinship between individuals X and Y and fxs and fxp are the kinships measured between X and the father and mother respectively of Y see Boyce 1983 for details of the algorithm itself e The number of pairs for which kinship coefficients are to be computed can become very large even with modest pedigree sizes For example the total number of pairs disregarding sex that can be formed from a Master File containing n 1 500 individuals is n n 1 2 1 124 250 In order for KINSHIP to compute coefficients for so many pairs it automatically subdivides the input file and sequentially processes it in smaller groups of individuals This requires the program to intersperse calculations with repeated reads and writes to a temporary disk file Consider carefully the need to compute kinship for large samples and be prepared for extended execution times in these cases e Choice of algorithm depends on the number of coefficients to be calculated and the complexity and generational depth of the pedigree The Stevens Boyce method must count the number of individ uals in each loop connecting Ego to a common ancestor Computations are minimal if Ego is not inbred but the task may be time consuming if Ego s parents are related in complex ways making the number of loops very large as may be the case for some domestic animals that are produced by repeated backcrossing The Quaas Hend
360. on the screen but calculations are limit ed to numerical items that is Data Types I R and D An error message will result if this requirement is not met Blank fields are treated as missing values and are not included in calculations Operands may be either numbers corresponding to items in the list on the screen or constants desig nated by a leading K or k The results of each operation are kept as a new item appended to the list corresponding to the end of the output record Operations may be chained that is the Item containing the result of a previous operation may be used as an operand in a subsequent calculation The random number generator used is a FORTRAN implementation of a hardware independent lin ear congruential algorithm described by R Sedgewick p 37 in Algorithms Addison Wesley Publishing Company Reading Massachusetts 1983 Calculations in CALC are carried out in single precision and computed output is limited to the PEDSYS default of five digits to the right of the decimal place However the precision of numbers up to 12 places to the right of the decimal may be changed reduced with the precision setting routines Precision of real numbers may not be set greater than that found in input values For example a five digit fraction may not be changed to six digits This limit does not apply to the change of integers to real numbers which permits the addition of up to five zeros to the right of the decimal
361. onding to items to be included in the combined record Enter A to include all items C to continue to next step gt 2 3 Here Sample Date and Hemoglobin Level Items 2 and 3 have been chosen Note also that the item selected to define record sets Item 1 Ego PID has been preselected and will be automatically become the first item of the combined record e Option Grouping Items by type within Output Records Normally data on output records consist of sets of item sequences whose order is determined by the order of selection from input records The result of this default is that items of any one type are interspersed with items of different types over the length of the record This order may be changed by the following option so that items of the same type are grouped together on the combined record Enter G to order the output record so that the same item types are grouped Enter RETURN to leave items on output records in the same order together as they were picked from input records gt e Option Choosing Record Sets Next an opportunity is provided to specify a source of identifiers of input record sets for which combined output records are to be constructed 11 2 e COMBINE April 19 1999 ETURN to combine items from all records in HEMOGLOB XMP Keyboard Unlinked File Example LOCUS Sub directory Enter number corresponding to alternate source of reco
362. onsisting of records containing minimally IDs for Ego Ego s parents and if required Ego s sex Individuals for which coefficients are to be calculated may be entered from either the keyboard or from a Proband Input File a file consisting of a list of either Sequential or Permanent IDs or may consist of all members of the input pedigree Output consists of a file containing IDs of Ego and Ego s parents if inbreeding has been calculated or Ego and another individual for kinship plus the appropriate coefficient Introductory Display EDSYS program KINSHIP Copyright 1992 1999 SFBR KINSHIP calculates coefficients of kinship phi for pairs of individuals or inbreeding coefficients F for single individuals by the Stevens Boyce or Quaas Henderson algorithm Stevens Boyce is usually more efficient for ped igrees of lower Quaas Henderson for higher than average kinship Inbreeding Kinship Inbreeding Kinship Stevens Boyce Stevens Boyce Quaas Henderson Quaas Henderson Enter number corresponding to choice of algorithm or Q to quit gt Any method chosen above produces a request for an input file containing one or more pedigrees that include individuals whose coefficients are to be calculated Unlinked pedigr fil Example Master File Enter number file name or O to quit gt 1 KINSHIP allows the use of input only from an indexed pedigree file that is one whose r
363. ontains the input output pathnames most recently accessed It is stored in the PedSys Progs folder and is read by any PEDSYS application when starting up to determine the path names for reading and writing PEDSYS files Double clicking this file launches the PedSys application and sets the input output paths to those specified on LASTPATH If this file is not found the user is asked to return to PedSys and select an input Data Folder June 10 1999 INSTALLATION and SETUP Macintosh OS F 3 PedSys settings is created and updated by the system to keep track of window placement font selections and other system wide parameters If this file is deleted it will be initialized with default values by the next active PEDSYS application If PEDSYS programs do not start up prop erly remove PedSys settings from the PedSys Progs folder and try again If the file was updated improperly or otherwise contains corrupted data it can interfere with program execution Fa 2 Installation PEDSYS for Macintosh can be obtained on CD ROM postal delivery or in self extracting archive files downloaded from the Southwest Foundation s web site Addresses are listed at the end of this document Installation procedures differ according to how the software is obtained e The PEDSYS CD ROM contains editions for Solaris DOS Windows and Macintosh and an Adobe Acrobat formatted version of the PEDSYS User s Manual Installation of the Macintosh edition from t
364. or Item number April 20 1999 IN or EX include or exclude Left justified SUBSET e 43 1 Relational Use FORTRAN conventions EQ LE LT GE GT or NE Value or string Left justified enclose substrings in matched single or double quotes Examples in 13 lt 19780630 includes all individuals born before 30 June 1978 but will also include individuals whose birth dates are blank ex 1 gt 10 includes only the first 10 individuals in the input file IN 18 NE X excludes individuals with Exit Code X e To compare one item with another begin the command line with an asterisk Example EX 13 EQ 17 excludes stillborn individuals also excludes individuals for which both birth date and death date are blank e To make a compound comparison begin second command line with AND or OR Example see command line in the Item List Display above e Substring comparison is limited to character data or dates that is items of Data Types Cand D as defined in the Code File comparison is case sensitive Only relationals EQ and NE are permitted in substring comparison Confirmation Display 1 INCLUDE Sex AND PEDIGREE Is this correct gt Standard Editing procedures are used with the addition of the following queries e If the subset is being defined by any item whose data type is I Ror D the following request will appear Interpret blank fields as zero Y N gt Responding with
365. or Ego and Ego s parents and sibs These conditions are fulfilled automatically if marker phenotypes are stored as a Linked Data File such aa QUANTGEN XMP If SEGCHECK is used when phenotypes are in an unlinked file choice 1 or 2 above the following instruction appears 1 Unlinked File 2 Example Master File Enter number or name of file containing pedigree information gt After the necessary files have been selected the following display appears from which a single locus may be selected for tabulation EGO Permanent ID 2 D1S1656 Genotypes 3 Sample No EGCHECK Select locus File D1S1656 Enter a number corresponding to the locus for which segregation tables are to be constructed or C to continue gt 2 May 21 1999 SEGCHECK e 37 1 Next the configuration of tables to be constructed is selected Select type of segregation table to be constructed Separate tables for fathers identified by father s PID Separate tables for mothers identified by mother s PID Separate tables for parental pairs identified by both PIDs Combined table for fathers with same genotype Combined table for mothers with same genotype Enter number above corresponding to choice gt 4 Here a table for sires by genotype has been selected Tables will contain a row for each mating type with columns representing offspring genotypes If 3 separate tables for parental pairs is chosen the follow
366. or new page lt n gt 1 1 to set top row gt or lt lt n gt to shift window I lt n gt 1 11 to set window L to lock columns N for new file F to find H for help Q to quit gt Note now that all dates are grouped together as are all hemoglobin levels and that the original order of items is preserved within group e Example 2 Combining Items from Input Records in a Single Entry File In the second example we show the results of combining items from input record sets derived from a Single entry file the Example Master File In this case key items defining record sets must appear on more than one record In Step 1 shown in the display below Sire and Dam Permanent ID have been chosen jointly to define sets so that items extracted from full sibships will be combined onto a single out put record 11 4 e COMBINE April 19 1999 EGO SEQUENTIAL ID ER OF OFFSPRING 15 Dam s Permanent ID SIRE S S ERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE ERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ FULL SIBSHIP SIZI 18 Exit Code EX ERNAL SIB SI EGO Permanent ID 19 Mate s Permanent ID EX ERNAL SIB SI Birth Date YYYYMMDD 20 PEDIGREE NUMBE EX L SIB SEQ 14 Sire s Permanent ID 21 GENERATION NUI COMBINI Select Identifiers File MASTER XMP Enter one or more numbers corr
367. ords are not shown even if IDs for FA and MO are present on the record e The instruction line will not contain commands associated with linked files PID S or e The status line at the top of the display will contain no reference to EGO PID e Records from unlinked files are written only to file show1 out For this example we wish to display file sort out which appears on the second line of the Primary File List shown at the beginning of this chapter Reusable Output Files are unlinked by definition As explained in Chapter III this file may be selected in two ways Entry of choice 1 from the Primary File List produces a Secondary File List of unlinked files containing sort out which may be selected by entering its corresponding number Alternatively since sort out already appears in the Primary File List as the most recently produced output file entry of choice 2 produces an immediate display of the first record in the file April 19 1999 SHOW e 40 5 File sort out Record 1 32 EGO Permanent ID ID067 Birth Date YYYYMMDD 1996 07 27 Sire s Permanent ID IDO15 Dam s Permanent ID IDO19 Sex M F or U Exit Date YYYYMM Exit Code zi ate s Permanent I PEDIGREE NUMBER GENERATION NUMBER Enter lt n gt 1 32 or lt n gt to select record L to lock items F to find W to write record N for new file H for help Q to quit gt Records may be acce
368. ords of the individual chosen will be seen The screen displayed below also results from entering s4 the SEQ of individual ID042 in the Example Master File ID ID042 4 5 VIAL SAMPLI Items 9 Recs 3 LIFO Page 1 1 FilePos 56 96 6 7 8 9 E ANIMAL PROJ COMMNT PNTR EN ID042 ID042 ID042 W218 S218 R218 1988 12 22 TYG 1980 10 03 9ML 1980 10 03 2ML OW OW lt n gt wu or lt n gt for new page or lt lt n gt to shift window Enter top row lock columns O to change order help Q to quit gt 41 2 e SHOWDATA STATUS STATUS D D D HL HL to set L to H for PID S lt n gt 1 32 I lt n gt 1 9 to switch files or lt n gt 1 96 to set window N for new file April 19 1999 lt n gt where lt n gt is a number corresponding to the position of a specific record in the file shown as FilePos in the right most position of the status line lt n gt must be in the range 1 through lt nrecs gt where lt nrecs gt is the number of records in the file currently selected for display This command results in a display of all records belonging to the PID found on the record specified Note that the same display can result from entry of more than one number For example entry of 4 6 or 56 produce the screen displayed above since there are records for ID042 in positions 4 6 and 56 in this file lt n gt l
369. osomal representation a Y in contrast to a a for example Such changes are likely to require substantial modification of genotype assignments Mode of inheritance is coded mnemonically as follows AUCD Autosomal codominant AUDR Autosomal dominant recessive XLCD X linked codominant XLDR X linked dominant recessive YL Y linked A Genotype Phenotype Map need not be created for autosomal codominant loci that adhere to the conventions given in Appendix C Rules for Genotype and Phenotype Nomenclature Nonetheless is it frequently helpful to generate a map for autosomal codominant loci using program GENOMAP because PEDSYS programs GENEFREO GENCHECK INFER and TRANSLAT will otherwise be forced to read through the entire Data File twice for each locus once to tally phenotypes and June 10 1999 GENOMAP e 21 11 again to do the analysis or transformation Presence of a map file eliminates the need for the tallying step and can significantly speed execution e To be accessible to PEDSYS programs that use it output file genomap tab should be renamed GENOMAP lt EXT gt and moved to the appropriate Data Directory Fa DYS391 PHE 21 12 e GENOMAP June 10 1999 Record 1 contains 1 4 locus mnemonics here ADA followed by integers denoting the number of alleles 3 phenotypes 6 and genotypic combinations 6 respectively and the symbol de
370. ot be left blank It is usually best not to duplicate the first and second mnemonic words within a given Code File as well d The last field column 54 contains the data type code C D I and R Character data is assumed if this field is left blank however it is a better idea to define this type Code C explicitly since it is difficult be sure that the record is the correct length without a visible character in column 54 The Master Code File Master Code Files are named CODE lt EXT gt where lt EXT gt upper case only is an extension identifying the population Here is an example of the Example Master Code File CODE XMP mpl aster Fil EGO SEQUENTIAL ID SIRE S SEQ DAM S SEQ FIRST OFFSPRING SEQ NEXT PATERNAL SIB SI NEXT MATERNAL SIB SI NEXT FULL SIB SEQ N P UMBER OF OFFSPRING ATERNAL SIBSHIP SIZE ATERNAL SIBSHIP SIZE FULL SIBSHIP SIZE EGO Permanent ID Birth Date YYYYMM Sire s Permanent I Dam s Permanent ID Sex M F or U Exit Date YYYYMMD Exit Code ate s Permanen PEDIGREE NUMBER GENERATION NUMBE 3 5 9 5 3 3 5 3 3 3 3 5 8 5 9 1 8 1 2 5 5 HHOAO0bDINTADIAOHHHHHHHHHHH A 8 e APPENDIX A June 12 1999 Important note mnemonic words defining some of the items in a Master File are invariant see Master File requirements above and the Standard Mnemonics File below Code Files
371. otypes for three loci have been assembled on records for each individual display from program BROWSE out Top record 1 32 2 3 4 5 DIS DIS D2S SAMPLE 1656 515 1329 NUMBE W236 W240 W238 W216 W218 W230 W232 ID015 B ID019 B 1D034 A IDO38 AE C B B U BB AA AC AC AC BD AB j Q Ab 1D042 1D045 1D047 tr D B w w di GI Enter lt n gt or lt n gt for new page lt n gt 1 32 to set top row gt or lt lt n gt to shift window I lt n gt 1 5 to set window L to lock columns T to change instructions N for new file F to find H for help Q to quit gt April 20 1999 INFER e 23 1 When an unlinked file has been selected INFER compares its Code File with entries in CODE STD for standard mnemonics identifying Ego and Ego s parents If the Code File does not contain mnemonics FA or SIRE and MO or DAM a pedigree file containing this information along with Ego PIDs that match those in the input file must be selected Pedigree information is not present in file merge out 1 Unlinked File 2 Example Master File Enter number of file containing pedigree gt 2 Here the Example Master File has been designated Next loci are selected for analysis 1 EGO Permanent ID 3 D1S515 Genotypes 5 Sample No 2 D1S1656 Genotypes 4 D2S1329 Genotypes INFER Select loci File merge out Enter number corresponding to the
372. our fields of this record contain a unique locus name which must be the same as the first four mnemonic words describing the locus in the Code File associated with the Data File containing phenotypic data c The fifth field contains an integer n enumerating the alleles found at this locus d The sixth field consists of an integer np enumerating the phenotypes expressed at this locus e The seventh field consists of an integer n enumerating all possible genotypes f The last field contains a four character alphabetic code specifying mode of inheritance These codes are AUCD Autosomal co dominant AUDR Autosomal dominant recessive XLCD X linked co dominant XLDR X linked dominant recessive YL Y linked A 20 e APPENDIX A June 12 1999 g The Allele Descriptor Record contains a list of the n alleles at this locus Its length is 6n h Strings representing alleles may be up to five printable characters in length Alphabetic symbols are case sensitive The third record is blank i The fourth and up to the 13th records carry labels for each of the n phenotypes Length of these records is 2n 13 There may be up to 10 such records in the file depending on the number of characters in the string making up the longest phenotype label j Characters in the strings making up phenotype labels are arranged vertically with each single character followed by a stroke 1 to provide visual separation between labels k A Genotype
373. ource for its Code File if specified has been en tered the following instruction appears here we will treat the Example Master File as if its record format is unknown by not specifying its Code File Some imported files keep data for a single individual on two or more contig uous records These data must be assembled into a single record in PEDSYS format Enter the number of input records that must be assembled into a single PEDSYS record or RETURN if the input file contains only a single record for each individual gt This feature makes it possible to transform multiple contiguous records into a single PEDSYS record for each individual ITEMIZE assumes that each in the sequence of multiple input records has the same format For example although it is not necessary for the first and second records in a group to have the same format all first records must be formatted identically etc Next the PEDSYS output file type is selected ITEMIZE will automatically assign Standard Mnemonics if the imported file is to be used as input for program INDEX to create a new Master Fil Enter H to assign human mnemonics N for nonhuman mnemonics C if neither applies April 20 1999 ITEMIZE e 24 1 Responses Hor N If the foreign file contains pedigree information and is to be submitted to program INDEX to create a PEDSYS Master File entry of h or n should be entered at this point This command
374. ource of pedigree information typically a Master File The Data File need not be linked Output segcheck tab contains segregation tables as specified when program is run Some examples of the content of this file are shown below Example 1 Table configuration choice 1 separate tables for fathers identified by PID tabulation without regard to offspring sex minimum 2 offspring per father all father s genotypes non informative matings excluded Segregation of TYPED FATHERS with at least 2 offspring MATINGS THAT SHOW SEGREGATION INFERRED PH ENOTYP ES INCLUDE LOCUS ADA PHENO TYPE ALLELES A B C Offspring genotypes Father Mother A A A B UNKNWN TOTAL A A TOTAL Father Offspring genotypes A A A B UNKNWN TOTAL 37 4 e SEGCHECK May 21 1999 Example 2 Table configuration choice 2 separate tables for mothers identified by PID tabulation by sex of offspring minimum 1 offspring per mother heterozygous mothers only informative matings only Segregation of ALL HETEROZYGOUS MOTHE th at least 1 offspring MATINGS THAT SHOW SEGREGATION INFERRE ENOTYPES INCLUDED LOCUS ADA PHENO TYPE ALLELES A B E Mot Offspring genotypes Mother Father A A A B A C B C C C UNKNWN TOTAL UNKNWN Mother Offspring genotypes
375. ove ABO ADA APOB Pvu2a Genotype CA1 andG6PD Phenotypes were selected previously for inclusion on output records The equal sign marking Item 5 indicates that Ego is a candidate for removal from the pedigree if ADA phenotype is invalid or missing from his or her record in the input file MARKERS XMP The plus signs marking Items 6 7 and 8 designate APOB Pvu2a Genotype and CA1 and G6PD Phenotypes as data that will be considered as a group The disposition of the data group is determined in the display that follows APOB Pvu2a Genotype CA1 Phenotype G6PD Phenotype Enter the minimum number of the 3 items above that must contain valid data in order for Ego to be included in the trimmed pedigr SZ The number 2 entered here specifies that Ego will be trimmed from the pedigree unless two of the three markers listed are present on his or her input data record Entry of 1 would eliminate Ego only if all three markers were absent simultaneously etc The absence of marks on Item 2 indicates that ABO phenotypic data including blanks or invalid entries will be not be used to determine Ego s eligibility for removal PIDs of Ego Sire and Dam are included automatically on the output record Note Although individuals with missing or invalid data are candidates for removal from the pedigree they may not in fact be removed if their position in the pedigree is required to link together other family members for which data is present Step 2
376. owed by a request for a list of IDs Enter P i f individuals are identified by Permanent IDs or S if by Sequential IDs gt p gt ID071 lt gt ID049 lt gt ID069 lt gt ID067 lt gt lt ID ID ID ID ID Enter Ego Permanent ID RETURN alone terminates entry Here Permanent IDs of four individuals have been entered Proband IDs read from a file Selection of proband ID is made from a Standard Item List Display EGO SEO UENTIAL ID 8 ER OF OFFSPRING Dam s Permanent ID SIE E S SEQ 9 PATERNAL SIBSHIP SIZE 16 Sex M F or U DAM S SEQ 10 MATERNAL SIBSHIP SIZE 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZE 18 Exit Code PA ERNAL SIB SEQ 12 EGO Permanent ID 19 Pedigree ID Number MA ERNAL SIB SEQ 13 Birth Date YYYYMMDD 20 Generation Number FU LL SIB SEQ 14 Sire s Permanent ID 21 Mate s Permanent ID File MASTE Identify PROBAND gt Enter number above corresponding to Proband ID Enter C to continue Here measurement of kinship coefficients between individuals identified by Ego Permanent ID has been specified e Option 4 Choice of fixed pairs of IDs from the pair composition menu limits kinship calculations to specific pairs of individuals whose IDs are either entered in pairs from the keyboard or read
377. play 1 Sex M F or U ENERATION NUMBER SORT Items to be sorted File MAST Is this correct gt The order of the sort is shown here Standard Editing procedures follow if N is entered Notes e Program SORT uses the Opt tech Sort routine which is the copyrighted property of Opt Tech Data Processing P O Box 678 Zephyr Cove NV 89448 and is distributed under license from the vendor e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example sort subset out Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file sort out may be used as input to program SORT Output sort out contains all records in the input file in sorted order sort cde defines the record struc ture of sort out Program limits A maximum of 20 items may be included in a compound sort iat 42 2 e SORT April 20 1999 SUBSET SUBSET generates compound subsets of records in any file for which an appropriate Code File has been constructed Introductory Display EDSYS program SUBSI ET Copyright 1992 EXAMPLE LOCUS Sub directory Unlinked File Enter number gt file name n 1999 SFBR constructed or TOT to Quit SUBSET generates compound subsets of records in any file for which an
378. position of the reset string are the same as for the control string described above Record format is A80 In this example a carriage return character lt 012 gt is sent to the printer followed by the Epson 286e reset sequence ESC ASCII character 0 signifies that no reset sequence is required for the console screen Control codes for more advanced printers can be quite complex Here is an example of a Device Control File set up for an OTC TriMax 850XL dot matrix line printer a Hewlett Packard LaserJet III a Sun LaserWriter PostScript printer and the console screen all attached to a Sun Microsystems computer 13 5 PGenLab LJ5 Main Lab LaserJet 5 091 064 pedsys bin nenscript R B L64 135 054 pedsys bin nenscript lr B fCourier9 L54 151 060 pedsys bin nenscript lr B fCourier8 L60 174 074 pedsys bin nenscript lr B fCourier7 L74 204 080 pedsys bin nenscript lr B fCourier6 L80 lt 000 gt 4 PGenLab LP Main Lab Line Printer 136 050 lt 018 gt lt 027 gt lt 080 gt 162 050 lt 018 gt lt 027 gt lt 077 gt 226 050 lt 015 gt lt 027 gt lt 080 gt 247 050 lt 015 gt lt 027 gt lt 077 gt lt 018 gt 1 CON Console Screen 000 000 lt 000 gt lt 000 gt 4 PGenLab Fuj Main Lab Line Printer 5 PGenLab LW Main Lab LaserWriterII 078 050 lt 027 gt amp 100 lt 027 gt 8U lt 027 gt amp a2L lt 027 gt s0p10h12v0s0b3T 170 050 lt 027 gt amp 1108D lt 027 gt 8U lt 027 gt
379. programs T Notes e Operators used to designate unacceptable values for character data Data Type C are limited to EQ and NE Operators for numerical data Data Types I R and D are EQ NE LT LE GT and GE e PEDTRIM minimally requires a pedigree file containing IDs for Ego and Ego s parents as input This need not be a Master File unless data are required from a linked Data File If an unlinked file is used its Code File must contain at least standard mnemonic EGO or ID In addition an unlinked file must have access to pedigree information This may be included either a in the file itself in 32 6 PEDTRIM July 8 1999 which case its Code File must also contain standard mnemonics FA SIRE and MO DAM or SEQ FSEQ SSEO and MSEQ DSEQ or b in an independent pedigree file whose Code File includes standard mnemonics for PIDs EGO or ID FA SIRE and MO DAM Output e The pedigree diagram below shows the results of trimming the larger of the two pedigrees in the Example Master File on the basis of the five markers specified above as critical data Below the IDs listed for each individual is a set of five alphanumeric symbols each representing a phenotype or genotype of one of the five genetic loci listed on the left hand side of the figure ABO ADA APOB CA1 and G6PD Empty pedigree symbols connected by broken lines represent those that have been removed Filled symbols represent individuals that remain after tri
380. provided to save by entering S edit by entering E or skip them altogether by entering X A request for another PID is then displayed etc Note To change an existing EGO PID a new record for EGO must be entered and the old record deleted using the ADD and DELETE features of ALTMASTR Command A Add new records to a Master File Procedures for adding records are similar to those described above for editing records except that an error message appears if an attempt is made to enter the PID of an individual already in the Master File Command D Delete records from a Master File The D command produces a request for the PID of the record to be deleted When this ID is entered the contents of the record are displayed for review ID ID069 I Birth Date YYYYMMDD 19961013 Sire s Permanent ID ID054 Dam s Permanent ID ID068 Sex M F or U M Exit Date YYYYMMDD Exit Code 0 ate s Permanent ID PEDIGREE NUMBER GENERATION NUMBER Delete this individual Y N This confirmation is required before the record is finally selected for deletion and a request for another PID is displayed etc da Starting a new Master File Before ALTMASTR can be run a Code File containing all items required for a Master File must have been created see Chapter 4 CREATING A PEDIGREE DATABASE This Code File must be named CODE lt EXT gt where lt EXT gt is an extension identifyi
381. put records 8 PEDSYS to CRI MAP format CRI MAP requires a number of header records in its input data files as well as PID and allele symbols in integer form Since CRI MAP is a linkage analysis program at least two genetic marker loci are required in its input EGO Permanent ID 6 ADA Phenotype 11 EGO SEQUENTIAL ID Sire s Permanent ID 7 APOB Pvu2a Genotype 12 SIRE S SEQ Dam s Permanent ID 8 Tot Ser Cholesterol 13 DAM S SEQ Sex M F or U 9 APOAI Level PEDIGREE NUMBER 10 Discrete Trait TRANSLAT Select locus RANSTEST XMP Enter numbers corresponding to at least two items containing loci for inclusion in output Required items have been pre selected Enter C to continue to next step gt 6 7 Items 4 5 and 11 13 are preselected and are protected from further change Items 6 through 9 represent data variables that potentially may be selected for inclusion in the output file although in this example only Items 6 and 7 would be appropriate as they are the only ones designated as genetic marker loci When selection of loci is complete the following display appears Enter RETURN to assume all loci are autosomal co dominant or enter name of alternate Genotype Phenotype Map file loci not listed in a map file are assumed to be autosomal co dominant gt Execution begins when the source of genotype phenotype translation has b
382. r 02 re enter item using ALTMASTR in ALTER mode Re run SETMASTR using the most recent Update and Master files see note on renaming and deleting these files Group 1 Mismatched Mnemonics A check is done to assure that mnemonics identifying items in UPDATE lt EXT gt correspond to those in the Code File associated with the Master File The following error is reported if update mnemonics do not match mnemonic fields in the appropriate Descriptor Record of CODE lt EXT gt lt ego gt Entry not changed lt mnel gt lt mne2 gt lt mne3 gt lt mne4 gt not valid mnemonics 11 where lt mnel gt etc are mnemonics identifying the item in file UPDATE lt EXT gt This error may occur either when adding a new individual or when making changes to a record previously entered in the Master File Probable cause is a change made to CODE lt EXT gt since the time it was used with ALTMASTR To correct the error re run SETMASTR using the previous Update and Master Files with the appropriate Code File Group 2 Duplicate Entries To prevent addition of duplicate entries for the same individual the Master File is searched for EGO PID If not found records in UPDATE lt EXT gt are searched from the beginning to the most recent April 20 1999 SETMASTR 39 3 update to determine whether a new record for EGO has already been entered during this session The error is reported if EGO is found in either list lt ego gt Record
383. r Interactive Mode e ALTERDAT usually creates Update Files lt filename gt UPD and or lt filename gt DEL each time it is run with the same Data File If Update Files with these names already exist at start up an opportunity is provided to exit the program and archive them or to overwrite them e If both deletions and batch additions have been made that is if ALTERDAT has produced both lt filename gt UPD and lt filename gt DEL both SETDATA and DELRECS must be run to complete the update process SETDATA should be run before DELRECS Output File lt filename gt UPD contains the following information UPDATE lt recno gt lt ID gt lt mnel gt lt mne2 gt lt mne3 gt lt mne4 gt lt newvalue gt UPDATE lt recno gt lt ID gt lt mnel gt lt mne2 gt lt mne3 gt lt mne4 gt lt newvalue gt NEW ENTRY lt iteml gt lt item2 gt lt itemn gt Where records containing the words UPDATE and NEW ENTRY are descriptor records that indi cate the type of change represented in the record immediately following Also included in the UPDATE descriptor record is lt recno gt the number of the Data File record to be changed The next rec ord begins with lt ID gt the ID of the Data File record to be changed This will be a Permanent ID Number if the file is linked or it will be the item designated as the identifier if the file is unlinked The ID is followed by all four mnemonic words identifying the
384. r and should not be deleted or moved CODE STD defines the standard field mnemonics used to create and verify Code files for a linked Master File record This file is referenced whenever a Master File is opened by a PEDSYS appli cation DEVICES contains the application display window dimensions set in PedSys as described later in this document and printer page limits used by the applications Tally List and Report all of which generate printed output Each of these programs enables the Page Setup command on the File menu allowing standard printing options such as Page Orientation and Reduction Enlargement to be specified when the program is first started and before each subsequent output file selection These settings are combined with the selected font size to determine the maximum text line width and number of lines that can be printed on a single page These limits are stored and referenced the next time List Tally or Report is run Default values are Portrait orientation and 100 Reduc tion Enlargement e The remaining support files are maintained by PEDSYS applications PATHWAY is created or updated by the application PedSys when a Data Folder is selected using the Path IN button or when a path to an output folder is set using Path OUT It is stored in the input Data Folder Double clicking this file or its alias activates the PedSys application and sets the I O paths to the pathnames stored on the clicked PATHWAY file LASTPATH c
385. r of MASTER XMP and examped may be helpful in this case Enter O to exit program RETURN to continue to next step gt Although this is not a fatal error it is usually best to exit the program and switch the order of files to be merged in this case Fa Selecting Items to be Included in Merged Records If Key Items are correct that is are identical in width and Data Type items to be included in the merged record are selected from Standard Item Lists first for the Target file April 19 1999 MERGE e 28 3 EGO S EO ENTIAL ID SIRE S S DAM S SE FIRST OFFSPRING SEQ EX PA ERNAL SIB SI 8 9 10 11 12 ER OF OFFSPRING ERNAL SIBSHIP SIZ IATERNAL SIBSHIP SIZ FULL SIBSHIP SIZI EGO Permanent ID U PA 15 16 17 1 181 19 Dam s Permanent ID M F or U YYYYMMDD Sex Date Code s Permanent ID 20 21 EX EX MATERNAL SIB SI FULL SIB SEQ 13 14 ED EN IGREE NUMBER ERATION NU Birth Date YYYYMMDD Sire s Permanent ID Items from TARGET file TARGET File MASTER XMP M ERGE order they are to C to continue above in th list all items Enter numbers corresponding to items shown be included in merged record Enter A to to next step gt and then for the
386. r the ID of the proband Once a proband ID has been entered Method 1 proceeds as follows Step 1 A nuclear family unit consisting of the proband the proband s parents full sibs one or more mates and all offspring This family unit forms the basis of a pedigree stored in the Output File and its members excluding the proband and his or her mates are used as input to subsequent steps if specified Mates are included in the unit but are not used as the basis for successive steps of family unit construction In the absence of inbreeding kin identified in Step 1 are related to the proband with a coefficient of kinship 6 0 25 The diagram below shows relatives of proband ID065 included in the pedigree after Step 1 27 4 e MAKEPED May 19 1999 18 17 16 ID045 1 1D034 1D077 ID070 ID054 ao r I o LI 20 21 IDO71 ID049 Proband LC Family members included after Step 1 11 ID047 ID068 IDO15 Pedigree Draw Step 2 If this step is specified family units are constructed for each of the proband s parents sibs and offspring and individuals not previously identified in Step 1 are added to the pedigree Kin identified in this step grandparents half sibs aunts uncles nieces nephews and grandchil dren are related to the proband with 0 125 The diagram below shows relatives of proband 1D065 included in the pedigree after Step 2 18 17 16 1D077 ID070 ID054 20 21 IDO71 ID049 Proband LI Family member
387. ranslat tab transtab cde and translat err Note e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example translat subset out References Almasy L Blangero J 1998 Multipoint quantitative trait linkage analysis in general pedigrees American Journal of Human Genetics 62 1198 1211 Green P Falls K Crooks S 1990 Documentation for CRI MAP Version 2 4 Department of Genetics Washington University School of Medicine St Louis MO 63110 Elston RC Bailey Wilson JE Bonney GE Keats BJ Wilson AF 1986 S A G E A package of computer programs to perform statistical analysis for genetic epidemiology Seventh International Congress of Human Genetics Berlin Abstracts p 389 Hasstedt SJ 1989 Pedigree Analysis Package Rev 3 0 Department of Human Genetics University of Utah Medical Center May 19 1999 TRANSLAT 45 13 Lange K Weeks D Boehnke M 1988 Programs for pedigree analysis Mendel Fisher and dGene Genetic Epidemiology 5 471 472 Lathrop GM Lalouel JM 1984 Easy calculation of lod scores and genetic risks on small computers American Journal of Human Genetics 81 3443 3446 Mamelka PM Dyke B MacCluer JW 1993 Pedigree Draw for the Apple Macintosh Population Genetics Laboratory Technical Report No 1 Southwest Foundation for Biomedical Research San Antonio TX 78284 Second edition 81 pp Program Limits A maximum of 500 items may
388. rches its Code File for the Standard Mnemonic EGO or ID If not found the program terminates with an error Selection of Data Items A Standard Item List is displayed separately for each file from which data records are taken in the order the files are selected In this example the Item List from the Marker Phenotype file is displayed first 1 Ego ID 3 APOB Pvu2a Genotype 5 APOAI Level 4 Tot Ser Cholestero 2 ADA Phenotype File QUANTGEN XMP REPORT Data items to be listed Enter numbers corresponding to DATA items shown above in the order they ar to appear across the page Enter A to list all items C to continue to next step gt An Item List Display from the next Data File if one has been selected appears when items from the previous Data File have been chosen 1 Ego 3 Hemoglobin Level 2 Sample Date 4 INTERNAL POINTER REPORT Data items to be listed File HEMOGLOB XMP Enter numbers corresponding to DATA items shown above in the order they ar to appear across the page Enter A to list all items C to continue to next step gt Data items will be printed in the order selected in the next display order as found in Header File in ascending order in descending order r corresponding to order that IDs should appear in list Data records are grouped according to the header Key Item that is EGO PID If a linked M
389. rcial data base systems 1 PEDSYS Master File records incorporate as data a set of pointers Sequential IDs that link each individual with key members of the nuclear family Thus the Master File carries its own indexing for family members making it possible to construct extended families very quickly and without the need to access additional files We have spent some effort to make screen displays and listings simple and easy to interpret but because the system is so frequently used to prepare data for other analysis programs PEDSYS out put is oriented principally toward the generation of files rather than prpoduction of elaborate reports PEDSYS programs are compiled containing no interpreted code A disadvantage of this approach is that the user cannot add new functions to pre existing programs as can be done with many commercial database systems On the other hand this program structure makes it easier to control and test the various functions and algorithms used as well as to assure consistency and simplicity Fe 1 2 INTRODUCTION April 20 1999 II CREATING A PEDIGREE DATABASE Under revision The simplicity of PEDSYS program operations depends on correct configuration of the file and directory structure The basic rules are 1 Master Files and their associated Data Files must be in the same directory 2 Each Master File or Data File must have an associated Code File 3 A Master File must have a Master Pointer
390. rd identifiers gt 1 Entry of RETURN results in extraction of items from all sets identified in the input Data File 1 allows extraction of items from selected sets whose identifiers are entered from the keyboard 2 4 allows extraction of items from selected sets whose identifiers are read from a separate file e Example 1 Combining Items from Input Records in a Multiple Entry File In our first example we show the results of selecting a single record set from file HEMOGLOB XMP by entering a PID from the keyboard Enter E ETURN alone starts execution gt ID015 Enter E URN alone starts execution gt To see the effects of COMBINE look first at the display from SHOWDATA below which shows the set of five records belonging to individual ID015 EMOGLOB XMP ID ID015 Items 4 Recs 5 LIFO Page 1 1 FilePos 1 238 1 2 3 4 EGO DATE hgb PNIR ID015 1988 05 27 14 ID015 1989 03 24 13 ID015 1990 01 24 12 IDOLS 1991 01 08 13 ID015 1993 05 06 12 Enter lt n gt or lt n gt for new page PID S lt n gt 1 32 or lt n gt 1 238 to set top row gt or lt lt n gt to shift window I lt n gt 1 4 to set window L to lock columns O to change order to switch files N for new file H for help Q to quit gt April 19 1999 COMBINE 11 3 The results of combining Items 2 and 3 for individual ID015 into a single record can be seen in the display from BROWSE
391. rdat The initial indicates that the descriptor line applies to an ordinary file The characters rwx are repeated twice indicating that the owner tom and group staff have full privileges while the last three characters r x specify that other users may read and execute but not write the files b Data Directories The owner and group associated with PEDSYS Master Files and Data Files need not be the same as those for Program Files A typical Data Directory entry for the Example Master File might be TEW E TE 1 bdyke genetics 3072 Jul 19 1998 MASTER XMP The initial indicates that the descriptor line applies to an ordinary file Read and write privi leges rw are given to the owner bdyke and group genetics while only read access is given to other users r Because this is a Master File execute privileges are not needed and a dash appears in the third position of each set of characters Note that PEDSYS Master Files and Data Files also can be assigned simple passwords with program DBFILER The security of these passwords depends in part on the security of the Directory File DBFILES in which they are kept c Data File Locking PEDSYS uses the Unix utility SCCS Source Code Control System or equivalent for file locking that is to keep more than one user with Data Directory write privileges from trying to update a Master File Data File or Code File at the same time SCCS protection may be implemented after installat
392. re individuals with their relatives The program constructs pedigrees in two ways a by assembling ascending and or descending geneal ogical trees of specified depth for each proband selected or b assembling family units parents full sibs mates and offspring for a single proband and for specified relatives The Output File generated by both methods is ordered by Permanent ID and duplicates are eliminated so that individuals appear only once which may merge pedigrees when multiple probands are selected The file from which ped igrees are generated may be either a Master File or an indexed pedigree file consisting of records con taining IDs for Ego and Ego s parents Sex etc Pedigrees may be constructed for probands entered from the keyboard or from a Proband Input File consisting of a list of either Sequential or Permanent IDs Introductory Display EDSYS program MAKEPED Copyright 1992 1999 SFBR MAKEPED constructs pedigrees a by extending genealogical links upward and or downward from one or more probands or b by starting with a single proband s nuclear family and extending successive links both vertically and laterally to relatives of the proband IMPORTANT The file from which the pedigr is generated must be an indexed pedigree file with an associated Master Pointer File Unlinked File 2 index out 3 Example Master File Enter number file name or Q to quit
393. reated Table is edited Program limits 100 conditional assignments IF statements Fa 34 12 PREPDRAW May 4 1999 REFORMAT Program REFORMAT is used to reformat join delete rearrange the order etc of items in records of a single Master File or Data File The program also makes it possible to add items consisting of blanks a character string and a series of sequential or randomly ordered numbe Introductory Display 1999 SFBR EDSYS program REFORMAT Copyright 1992 TS Eos OF EFORMAT is used to reformat delete items in records of a single Master File or Data File join rearrange th Unlinked File EXAMP L LOCUS Sub directory fil Enter number or O to quit gt name Next a Standard Item List is shown 15 16 8 NU 9 PA ER OF OFFSPRING ERNAL SIBSHIP SIZ 10 MATERNAL SIBSHIP SIZ 11 FULL SIBSHIP SIZI 12 EGO Permanent ID 13 Birth Date YYYYMMDD 14 Sire s Permanent ID ENTIAL ID EGO SEQ SIRE S S DAM S SE FIRST OFFSPRING SI EXT PATERNAL SIB SI EXT MATERNAL SIB SI EXT FULL SIB SEQ EO 19 20 21 17 I 18 I order I Dam s Permanent ID Sex M F or U it Date YYYYMMDD it Code ate s Permanent ID EDIGREE NUMBER ENERATION NU R RMAT Items to be included File MAST
394. record 25 lt ego gt Entry not changed internal pointer not consistent with PID 26 where lt ego gt is the PID of the record to be updated in lt FILENAME gt UPD Probable cause of Error 25 is incorrect specification of Data File Type Single or Double entry in the Directory File Probable cause of Error 26 is prior deletion of a data record which might occur if program DELRECS has been run before program SETDATA April 20 1999 SETDATA e 38 3 Notes a e The number of each error appears in parentheses at the end of the error record e All errors are best corrected with program ALTERDAT Files Input Output Any PEDSYS Data File and its associated Code File lt filename gt UPD produced by program ALTERDAT containing changes or additions to Data File records MPOINT lt EXT gt and DPOINT lt EXT gt are required if new records are added to an existing Data File which is linked to a Master File lt filename gt lt ext gt is the new or updated Data File produced by the program lt filename gt OLD is a backup copy of the input Data File produced if lt filename gt lt ext gt is generated as the result of changes and or additions to the input Data File lt filename gt OLD is not produced if lt filename gt lt ext gt is newly created lt filename gt OUP is a backup copy of lt filename gt UPD setdata log contains a record of each change that was successfully completed by the program setd
395. record is examined however it is sometimes possible to miss an infrequent non blank entry Choice of option B avoids this possibility by preserving skipped fields if they contain a non blank character on any record in the file If upon EXIT there are characters remaining in the input Data Record that have not been assigned to Data Items the following instruction is displayed before files are saved Enter D to DISCARD unassigned portion of input record S to SAVE unassigned portion of input record Q to QUIT program without saving output Saving the unassigned portion of the input Data Records along with skipped fields as described above makes it possible to interrupt execution of the program and to return to assignment of characters to PEDSYS Data Items at a later time Input Data Records like PEDSYS records are limited to 1024 characters in length Unlike PEDSYS records however they may contain more than 100 variables Thus it may be necessary to use ITEMIZE on the same input file more than once assigning as many characters as one can to 100 PEDSYS Items and then saving the unassigned portion of the record as described above Program REFORMAT can then be used to divide itemize out records into two files and the file containing the unassigned portion may then be run through ITEMIZE again In order for PEDSYS programs to access the unassigned portion of the record however ITEMIZE automatically assigns it PEDSYS format
396. rectory To change this default a short optional file containing disk drive and directory specifications may be placed in each working directory Unix and MS DOS or Data Directory Macintosh PEDSYS programs use the routings specified in this file if it is present rather than the default The file must be named PATHWAY and may contain one or two records defining input and output data paths as needed This file is best created with program setpath although with care any text editor may be used For example a Data Path File containing the following records pedsys example home users bdyke would direct PEDSYS programs to read input from the Example Data Directory and send output files to home users bdyke Note Temporary System File LASTFILE TMP is always directed to the current Data Directory and is not affected by the output path specified in the Data Path File References Dyke B 1993 Basic data standards for primate colonies American Journal of Primatology 29 125 143 Dyke B Mamelka PM 1989 ACMP an Animal Colony Management Package User s Guide Population Genetics Laboratory Technical Report No 3 Southwest Foundation for Biomedical Research San Antonio TX 78228 sa June 12 1999 APPENDIX A e A 23 A 24 e APPENDIX A June 12 1999 Appendix E INSTALLATION and SETUP Sun Microsystems Unix Solaris 2 5 In this appendix we describe directory organization installation procedures and file access and per
397. red as follows Given Denied read r write w execute x Ownership group membership and permissions are usually assigned by the Unix Systems Manager Examples of typical Unix directory entries are shown below a Program Directories The owner of a PEDSYS Program Directory and its files is usually the individual who has the major responsibility for installing and maintaining these files and who thus must have unrestricted read write and execute privileges in the PEDSYS account Additional selected users may be assigned a group that has some set of privileges whereas most other users are given only read and execute access A typical entry for a Program Directory might be drwxrwxr x 8 tom staff 3702 Jan 6 11 19 The initial d indicates that the descriptor line applies to a directory The characters rwx are repeated twice indicating that the owner tom and group staff have full access to this directory Here read access refers to permission to list the files in the directory write access makes it possible to add a file to the directory while the execute privilege makes it possible to open the directory for access The last set of three characters r x specifies that other users may open the directory and list existing files but may not add new files to it E 4 e INSTALLATION and SETUP Solaris 2 5 June 10 1999 A typical Program Directory entry for program ALTERDAT might be rwxrwxr x 1 tom staff 2039088 Jan 6 11 19 alte
398. ree Database 10 December 1996 available in the form of a foreign that is non PEDSYS ASCII text file containing a single record for each individual Contents and format of these records should be the same as those listed above for keyboard data entry Step 1 Procedures for creating a Master File from a foreign data file will vary depending on the record format of the foreign data file Character delimited format Data are frequently transferred between computers or application programs using a simple format by which individual items are separated by specially designated field separators usually the tab character ASCII code 09 comma ASCII code 44 or blank ASCII code 32 If your data are formatted this way use program TRANSLAT selecting the Delimited field to PEDSYS option in the introductory screen display choosing the name of the foreign file when prompted and letting the program create a Code File based on input data field widths This operation will produce an output Data File translat out in PEDSYS format and a rudimentary Code File translat cde in which field widths and data types are correctly specified but item descriptors and mnemonics are numbered but otherwise undefined Item descriptors and mnemonics in translat cde can then be modified with program CODE to better describe the data in translat out Fixed format The safest way to create a Master File from a foreign file having fixed format records is to run progra
399. ree can be supplied by another file GENOMAP lt EXT gt the Phenotype Genotype Map File contains information on mode of inher itance forms of allele and phenotype symbols and the relationship between genotypes and phenotypes for dominant and or X linked phenotypes An alternate Phenotype Genotype Map File may be specified as input inferl out consists of a record for each individual represented in the input locus data file Each record contains all the items of the input locus file in their original order with the inferred phenotype or genotype appended at the end infer2 out contains a record for each individual in the Master File or pedigree file for which an original phenotype is available or for which a phenotype or genotype can be inferred inferl cde and infer2 cde define the record structures of inferl out and infer2 out respectively infererr out contains a record for each individual for which a genotype cannot be inferred be cause of inconsistencies between Ego and one parent infererr cde defines the record structure of infererr out 2 Multiple loci from file in the LOCUS Sub directory Input Output A special purpose file containing selected names of locus files in the LOCUS Sub directory plus the locus files and their associated Code Files A file such as a Master File containing pedigree data GENOMAP lt EXT gt or an alternate Phenotype Genotype Map File I lt locusfilename gt contains records for
400. referred to as a variable Entry The actual contents of an item Also referred to as a value For example we refer to Birth Date as an item of information found in the thirteenth field of a Master File record The number 19821103 corresponding to November 3 1982 might represent the Birth Date entry for a particular individual Ego Generally the term Ego refers to an individual from which genealogical relations are determined in a pedigree In some cases this may be equivalent to the medical genetics term proband or the individ ual whose phenotype motivated construction of the pedigree In PEDSYS terminology the individual whose vital statistics appears on each Master File record is referred to as Ego sa B Data Types Information in PEDSYS files is stored as character data However these data are interpreted by PEDSYS programs according to codes specified in a Code File Data items may be of the following types shown with their codes C Any printable character ASCII characters 32 126 Normally these will be left justified but because all blanks are honored right justification may be forced I Numerical integers Blanks are treated as zeros except in programs CALC and TALLY where blanks may signify missing values Integers are right justified PEDSYS integer input from disk or keyboard output to disk or printer and computations internal to the processor are limited to numbers in the range 2 147 483 648 to 2 147 48
401. remains unaffected as Data Files are changed b A number of programs have been designed specifically to automate the task of merging reformatting and transforming data April 20 1999 INTRODUCTION 1 1 5 We feel that large scale software packages must not be dependent on any one type of computer or operating system Consequently PEDSYS programs are written principally in ANSI Standard FORTRAN 77 with numerous functions in ANSI Standard C Machine dependent code has been isolated and identified in the few cases where it has not been possible to avoid altogether chiefly file access and screen display routines Written originally for a time sharing Concurrent Computer Perkin Elmer 3210 the system has been adapted for MS DOS Microsoft Windoes Sun Microsystems Unix SunOS 4 6 and Solaris Linux and the Apple Macintosh OS System 6 07 and higher PEDSYS has grown and evolved over the years in response to the suggestions of the scientists and technicians who have used the system New programs are first written as quickly as possible in response to the needs of a specific research question Previously developed program modules or algo rithms are incorporated wherever possible but refinements are added only as users gain experience with the program This approach has resulted in programs that meet a broad range of requirements for pedigree data management Three features distinguish the PEDSYS database management system from most comme
402. rors occur only when making changes to a record previously entered in the Master File Probable causes are a the PID appears neither in the Master File nor in UPDATE lt EXT gt prior to this attempted change or b an incorrect PID in UPDATE lt EXT gt presumably at time of keyboard entry To correct the error If a first enter record for missing individual using ALTMASTR in ADD mode and then re enter the change in EGO s record using ALTMASTR in ALTER mode If b re enter change with correct PID using ALTMASTR in ALTER mode Re run SETMASTR using most recent Update and Master Files see note on renaming and deleting these files Group 4 Inconsistent Gender Assignments Before making changes to parental PIDs SETMASTR verifies that the sex of individuals listed as parents in the Update File is consistent with their sex as it appears in the Master File This check is done by searching the Master File and records in UPDATE lt EXT gt that have already been processed for the appropriate parental PID Errors are reported as follows if sex assignments are found to be inconsistent lt ego gt SIRE PID not changed lt newsire gt listed as female in MF 41 lt ego gt DAM PID not changed lt newdam gt listed as male in MF lt ego gt lt parntyp gt not assigned lt parntid gt listed as lt sex gt in MF 43 where lt newsire gt is the SIRE PID lt newdam gt is the DAM PID and lt parntyp gt is the t
403. rs gt Pedigree Draw 4 4 allows up to five 24 character text fields per record Items selected from the Item List Display are entered into these fields left justified Inclusion of these items is optional Note that Sequential IDs of Ego and parents and SEX are pre selected TRANSLAT also searches the input Code File for the mnemonics NOREP and SYMBOL and will copy these items into the appropriate fields of Pedigree Draw records Default values are inserted into these fields if these mnemonics are not found in the Code File 4 Pedigree Draw 4 4 to PEDSYS When Pedigree Draw to PEDSYS format translation is selected a request for the appropriate file name is shown All Pedigree Draw fields are translated into PEDSYS format These include items representing data added by Pedigree Draw programs a Number of individuals represented This item is labeled Number represented and given the mnemonic NOREP in output Code File translat cde b Symbol codes This item is labeled Symbol codes and given the mnemonic SYMBOL in output Code File translat cde The Pedigree Draw header record is not included in PEDSYS output file translat out but the pedigree title is copied from the header to the PEDSYS Code File Label Record Notes on PEDSYS Pedigree Draw 4 4 Conversion This conversion applies only to records for Pedigree Draw Version 44 Conversion between PEDSYS and Pedigree Draw Version 5 0 files is done in program PREPDR
404. rting at the top of the display The remaining items are not displayed 40 4 e SHOW April 19 1999 ID ID063 File MASTI Record 10 32 Page 1 1 EGO SIRE DAM EGO Permanent ID ID063 ID038 ID042 Birth Date YYYYM 1980 11 28 1974 05 05 1975 00 00 Sire s Permanent I ID038 Dam s Permanent ID ID042 Sex M F or U M M F Exit Date YYYYMMD 1996 12 23 1996 11 14 Exit Code 1 1 ate s Permanent I ID042 ID038 Enter PID S lt n gt 1 32 lt n gt 1 32 or lt n gt to select record L to lock items to switch files F to find W to write record N for new file H for help Q to quit gt e Items in locked rows form a subset of other items displayed and are positioned in order of selection from the top of the screen They remain visible in their locked positions from one record to the next e Unlike program BROWSE unlocked items are not displayed These can be redisplayed by reissuing the lock command and selecting items as required e Rows may also be locked by entering L followed by an Item Number For example rows can be ordered in the same sequence as shown in the display above by entering L12 19 e Rows may be unlocked that is returned to their original order by entering LO Sa 2 Displaying Unlinked Files The display of information from an unlinked file is different from that of a linked file in that e Information for only one record will be displayed That is parental rec
405. ry File DBFILES and linked to a Master File e lt FILENAME gt lt EXT gt the Data File to be linked must be named in DBFILES That is there must be a Data File Descriptor Record for lt FILENAME gt lt EXT gt that contains an appropriate file extension see Note k in the section on The Directory File Appendix A a file name Note 1 a label Note m a pointer position number Note n a multiple entry indicator Note 0 a Log File indicator Note p and passwords as needed Note q The Data File Count Record must also reflect the presence of the file Note i e DPOINT lt EXT gt The Data Pointer File Appendix A will be created by DATALINK if it does not exist e A new pointer will be appended to each record in DPOINT lt EXT gt at the time lt FILENAME gt lt EXT gt is first linked to a Master File Subsequently the pointer position number specified in the relevant Data File Descriptor Record of DBFILES see Note n in the section on The Directory File Appendix A will determine the pointers to be updated e DATALINK creates an updated version of a preexisting version of DPOINT lt EXT gt if it exists but saves a copy of the old file as DPOINT OLD Warning Prior versions of DPOINT OLD will be deleted and over written each time DATALINK is run unless they have been renamed e DATALINK creates an updated version of lt FILENAME gt lt EXT gt if it is a Multiple entry Data File but saves a copy of the old file as lt F
406. s Project Code Comments INTERNAL POINTER D Enter to DELETE 4 10 e ALTERDAT to advance through multiple records or X to gt ID069 W250 19980414 TYG HLM New map 95 DA to DELETE ALL of EGO s records lt n gt EXIT without deleting record April 20 1999 Again when all deletions have been entered ALTERDAT is ended with the Q command and pro gram DELRECS is run to complete the deletion process DELRECS automatically adjusts the pointers to internally linked records when deletions are made in a linked Multiple entry Data File see note o in the Notes on DBFILES Record Formats section in Appendix A Fa Two of the commands controlling editing features of ALTERDAT commands O and L operate identically with Single and Multiple entry files The confirmation command F is slightly different in that it is unneccesary to re enter IDs for each record of a multiple record set when confirmation is off Two additional commands T and B unique to editing Multiple entry files are provided Command T Set template when adding new records When adding a record to a multiple entry record set the default initial state is for all its items to be blank on the new record The template function makes it possible to change this initial state by fil ling in items on the new record with data taken from the most recently entered record in the set Thus the templ
407. s Permanent ID 8 Tot Ser Cholesterol 13 DAM S SEQ Sex M F or U 9 APOAI Level PEDIGREE NUMBER 10 Discrete Trait TRANSLAT Select Covariates RANSTEST XMP Enter numbers corresponding to items containing COVARIATES to be included in output Required items have been pre selected Enter C to continue to next step gt At this point TRANSLAT begins execution Notes on SOLAR MIXED format conversion e PEDNO and IBDID fields required PROBND field optional e The SEX field must only be 1 character wide and be an integer field e CONTINUOUS TRAITS DISCRETE TRAITS and COVARIATES may not be represented as Data Type C e CONTINUOUS TRAITS may not be discrete DISCRETE TRAITS may not be continuous e Execution is terminated if DISCRETE TRAIT value is other than blank 0 or 1 e COVARIATES may not also be selected as TRAITS e The PROBND field is optional if present a it must contain a non zero non blank value and b a FOCAL PROBAND TRAIT field containing a non blank continuous or discrete value for each proband is required e FOCAL PROBAND TRAIT has to have been picked as continuous or discrete trait e At least one individual per family must have complete data For any family in which this is not the case the following message is written to fine translat err Family not included for lack of quantitative data Fa Files Input PEDSYS to
408. s an Exit Code Item 18 equal to 1 and the command line contains an entry that will select individual ID015 as the proband a diagonal arrow pointing to the symbol designating EGO Rules of pattern assignment are the same as those governing conditional item modification in program NEWITEM Graphic representation of Palette 1 is shown in the left hand panel below May 4 1999 PREPDRAW e 34 3 Deceased C Proband Ti Trait 1 T1 T3 Li Affected Monozygotie Twin T2 Trait 2 T2 T4 Pregnancy Dizygotic Twin T3 Trait 3 T2 T3 T4 T4 Trait 4 T1 T3 T4 Miscarriage Zygosity Unknown Stillbirth O Adopted Ti T2 T1 T2 T4 PI pats unmarried T2 T3 T1 T2 T3 T3 T4 T1 T2 T3 T4 Bg f E E i afrai Ti T4 Unknown PER a 7 fa I E gt HELPE Misc Code Custom Picture 2 nz Custom cel Palette 1 Standard Types Palette 2 Traits quadrants FEREREEE Trait e Note No more than a total of four symbol types may be assigned to the same individual from Palette 1 and Palette 4 combined Additional attributes may be assigned to these symbols from other palettes for a total of six altogether Choice of Palette 2 shown in the right hand panel of the figure above results in the following display INTERNAL SIBSHIP SIZ ate s Permanent ID FULL SIBSHIP SIZE PEDIGREE NUMBER EGO Permanent ID GENERATION NUMBER Birth Date YYYYMMDD Ego ID Sire s Permanent ID ADA Phenotype Dam s Permanent ID APOB Pvu2a Genotype
409. s been added to the XMP Directory A log of changes alterdat log will be created and automatically updated each time this file is modified with program ALTERDAT and two passwords have been assigned Addition of a Linked Data File Descriptor Record adds a new column of pointers to file DPOINT lt EXT gt when program DATALINK is run Note a Linked Data File Descriptor Record cannot be added unless DBFILES contains an appro priate Master File Descriptor Record and the Master File itself is present in the Directory U OptionU results in addition to DBFILES of a Descriptor Record for an unlinked Data File This operation requires only that a file name be supplied Although a file name is added to DBFILES no actual file is created in the directory S Option S results in addition to DBFILES of a Descriptor Record for a sub directory This opera tion requires only that a sub directory name be supplied Addition of a sub directory name to DBFILES results in creation of a sub directory in the current parent directory Fa D DELETE Deletion of a Descriptor Record from DBFILES removes the corresponding file name from the PEDSYS File List Display but does not affect the file itself Removal of one unlinked file does not affect other files Removal of a Linked Data File has the effect of removing the corresponding column of pointers on records in file DPOINT lt EXT gt ETE DBFILES entry 1 Example LOCUS Sub directory
410. s described below SHOWDATA treats single entry files in much the same way as does program BROWSE except that unlike BROWSE only one record is displayed at a time 1 Displaying Linked Data Files In the example below the Blood Sample Inventory file and the Hemoglobin Levels file have been marked with an asterisk indicating that they have been selected for display The order of selection and display is usually not critical since switching between files is cyclical Linked files Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels ore than one LINKED file may be selected for repeated sequential display Enter numbers corresponding to file s above in the order they are to b shown Enter RETURN alone to continue to next step gt Entry of RETURN results in a display of records belonging to the first individual in the Sample Inventory File At the top of the screen a status line appears showing the file name SAMPLES XMP the PID of the first individual in the file 1D097 the number of items per record 9 the number of April 19 1999 SHOWDATA e 41 1 records belonging to the individual selected 3 the order of access LIFO the number of pages required to display these records 1 1 and the position of the record currently selected in the display 1 96 The display window extends to the right for a are unlocked ID ID097 3 DATI 4 5 VIAL S
411. s included after Step 2 May 19 1999 ID068 1D015 Pedigree Draw MAKEPED e 27 5 Step 3 In this and subsequent steps if specified family units are formed for each relative newly iden tified in the previous step etc In general measured between the proband and kin newly iden tified in each step will be equal to 1 2 STEP 1 providing the pedigree is not inbred Files Input Any Master File or indexed pedigree file and Master Pointer File Input Data File or console keyboard Output makeped out contains one or more pedigrees connecting probands to their relatives according to limits specified on input makeped ego contains records identifying probands for which pedigrees were constructed makeped cde defines the record structure of makeped out and makeped ego makeped err contains a proband IDs entered from an input file that are not found in the input pedigree file and b IDs of individuals whose sex is unknown SE 27 6 e MAKEPED May 19 1999 MERGE Program MERGE assembles single records for individuals from information kept in two separate Data Files The principal output file is created by adding to records in a Target file the first file accessed selected items copied from records in a Donor file the second file accessed Introductory Display EDSYS program MERGE Copyright 1992 1999 SFBR MERGE assembles single records for individuals from information kept in two separate D
412. s useful to separate individuals or pairs for which coefficients are zero from those whose coefficients are non zero This option is provided for in the following display that appears before execution of the program begins Save all output records in file KINSHIP OUT Discard output records with zero coefficients Save records with non zero coefficients in KINSHIP OUT coefficients in NOKINSHP OUT Zero Enter number corresponding to choice gt 1 e To conserve computing time KINSHIP skips calculations and assigns a zero coefficient of kinship between two individuals if they do not belong to the same pedigree that is if they do not have the same pedigree number KINSHIP checks to see if the mnemonic PEDNO appears in the pedigree Code File indicating that the file has been processed by program COUNTPED If the mnemonic is present the following query appears as a reminder that COUNTPED output may not be valid if records have been added or removed from the pedigree file after the program has been run Execution speed can be increased by limiting calculations to pairs belonging to the same pedigree This should be done only if records have not been add ed or removed from the Master File after program COUNTPED was last run and current pedigr identification numbers PEDNOs are certain to be valid Enter L to limit calculations to pairs in th PEDNOs RETURN to calculate kinship without regard to PEDNO
413. se 4 5 the Permanent ID that must appear on each record If this is not the case change the mnemonic as needed Note If you are sure that the Code File describing the structure of the foreign file is correct Step 1 may be skipped This shortcut is not advised however Step 2 As needed run file itemize out through program REFORMAT if the PID is not the first item in the records or if items require removal or rearrangement Step 3 Run a spot check of records in translat out or itemize out using program BROWSE or SHOW paying particular attention to records at the beginning and the end of the file If data on the records appear to be correct go on to Step 4 If data are not correct it may be necessary to a Modify the format of records in the file using program CODE b Force records to conform to the format specified in translat cde or itemize cde by running the input file through program REFORMAT with all items selected for output c Edit records using program ALTERDAT or d Re submit the original data to program ITEMIZE Step 4 Rename output files itemize out or reformat out and itemize out or reformat cde as lt FILENAME gt lt EXT gt and lt FILENAME gt CDE after archiving or deleting the original files of the same name and then run program DBFILER to modify the Directory File by adding the name of the new Data File to the Linked Data File list Step 5 Run program DATALINK entering the number corresponding
414. selection of loci for analysis and processing File merge out choice 2 above shown below is an example of multiple genotypes or phenotypes in an unlinked file display from program BROWSE out Top record 1 32 2 3 4 5 6 SIRE DIS DIS D2S SAI 515 1329 NUMBE D015 ID062 BB E W236 D068 ID062 AC W242 D054 ID063 CC E W234 D070 ID063 CC EE W214 D077 ID063 E AC E W216 D067 IDO15 AB E W246 AB CD D071 ID045 W244 D049 ID045 1 W248 D069 ID054 AC W250 H EH E A Eh H H GLH Enter lt n gt or lt n gt for new page lt n gt 1 32 to set top row gt or lt lt n gt to shift window I lt n gt 1 5 to set window L to lock columns N for new file F to find H for help Q to quit gt When an unlinked file has been selected DOWNCODE compares its Code File with entries in CODE STD for standard mnemonics identifying Ego and Ego s parents If the standard mnemonics FA April 19 1999 DOWNCODE e 17 1 or SIRE and MO or DAM are found in the input Code File the following query appears Use pedigree information found in merge out Y N gt If the answer is N or if the Code File does not contain standard mnemonics the following display appears Unlinked file Example Master File Enter number or name of file containing pedigree gt 2 Here the Example Master file has been chosen When a source of pedigree information has been sel e
415. send printed output In this example two devices have been specified Columns 3 through 80 of this record are ignored by program LIST and it is useful to use this space to define the purpose of the record as has been done in this example z These records begin with a device name which in the case of MS DOS must be one of the Reserved Names CON PRN LPT1 LPT2 LPT3 AUX COM1 COM2 or NUL This is followed by an integer specifying the number of character fonts available to the device maximum nine Format of the record is A7 1X I1 1X A30 The console screen should be the last device listed in DEVICES In this example PRN the first parallel printer with four fonts and CON the console screen with one font have been selected Columns 11 through 40 of this record are used as entries in the device control menu displayed by programs LIST REPORT and TALLY c Following each record specifying a device name comes one or more records one for each font that control page format and font setup This record consists first of two integers specifying the maximum number of characters in the printed line and the maximum number of records per page respectively These numbers are followed by a control string 72 characters maximum that can be used to initialize the printer and font Elements of this string are printable ASCII characters enclosed in double quotes and decimal equivalents of ASCII characters represented by a three digit i
416. sensitive and by convention executable file names are upper case The Master File The Master File consists of records containing basic information about individuals in a population The most fundamental items in each record are Permanent IDs PIDs of Ego the individual described A 4 e APPENDIX A June 12 1999 by the record and his or her parents Permanent IDs are designated as character data that is they need not be numerical and usually form an unordered list in the Master File To eliminate the need to make repeated time consuming searches through the entire list of unordered Permanent IDs when processing extended pedigrees PEDSYS creates Sequential ID numbers for Ego and selected members of Ego s nuclear family Sequential IDs the first seven items in a Master File serve as pointers record numbers designating the location of records of these family members in the Master File This scheme permits very rapid construction and analysis of large pedigrees since each individual record contains pre determined links to records of ascending father and mother descending first offspring and lateral relatives maternal paternal and full sibs Master Files may be created in two ways e A new Master File may be started by entering basic information about each individual from the keyboard using PEDSYS program ALTMASTR This program produces a specially formatted temporary update file that is used as input to program SETMASTR SETMAS
417. sequence If the cut set size for the nuclear family is greater than 1 additional linking individuals may be relatives of a family member who are also members of families that have not yet been processed Note that each record in the output file corresponds to a nuclear family in the input file Founder Status 0 indicates that both parents of an individual are known status 1 indicates that neither parent is known April 22 1999 PEELSEQ e 33 1 The table below shows the contents of output file peelseq tab giving the peel sequence generated from the Example Master File formatted for input to PAP 1 t 0 1 1 0 0 1 1 1 1 0 0 0 Po oR FE PR OOo Fo A pedigree diagram of the Example Master File from which the peel sequence was computed is shown below 3 2 27 26 25 23 ID038 ID056 ID083 ID080 ID097 ID095 O 29 24 ID109 ID111 9 30 ID019 1D113 Pedigree Draw The table below shows the contents of file peelseq2 tab in which for ease of interpretation PIDs are substituted for the Sequential IDs required by PAP Except for this substitution entries in this table are identical to those in output file peelseq tab 33 2 e PEELSEQ April 22 1999 1 ID047 ID049 1 1 IDO15 1 ID065 ID068 1 ID068 1 ID054 1D070 IDO77 2 ID065 ID063 2 ID042 ID065 ID109 ID103 ID109 ID109 rPOoOoOrRPRrRPRrRrRFOOOOrF OF HHHHHHHHHHHHHH If the program executes successfully it terminates with the follo
418. ssed by entering any number between 1 and lt nrecs gt where the number refers to the position of the record in the file In the example above the counter on the status line of the display reads Record 1 of 32 so that lt nrecs gt 32 and 1 lt lt n gt lt 32 It is also possible to precede the number with as explained above but this is not necessary The remaining command line functions L F N W X and P when more than one page is required to see the full record operate as described above z The Find function The Find function can be activated in one of two ways Entering F alone at the command line results in a Standard Item List with a request for the value sought for the particular item in EGO s record When this has been entered instructions for starting the search are given 1 Ego ID 3 APOB Pvu2a Genotype 5 APOAI Level 2 ADA Phenotype 4 Tot Ser Cholestero Enter item number relational EQ or NE and value sought Enclose sub strings in quotes gt 4 eq 140 Enter record number at which to start search 1 32 or RETURN to start at current record 1 gt In this example the Markers Quant P types file will be searched for the first record in which Total Serum Cholesterol Item 4 has the value 140 When a record containing the item sought is found it is displayed in full 40 6 SHOW April 19 1999 ID ID067 File QUANTGEN Record 4 32 SIRE Ego I
419. startup shortcut program name followed by a blank and an input file name may be used to start this program Example combine subset out April 19 1999 Files Input Any Data File containing more that one record with the same identifier and an associated Code File and optionally the console keyboard or an input file containing IDs of individuals whose records are to be combined Output combine out contains one record for each individual for which Multiple entry Data records exist combine cde defines the record structure of combine out combine err contains information about records that cannot be successfully combined that is by identifiers entered from keyboard entry or other alternate source and IDs of output records longer than 1024 characters Fa April 19 1999 COMBINE 11 7 11 8 COMBINE April 19 1999 COUNTPED Program COUNTPED 1 identifies genealogical links in a file and assigns numbers to each individ ual corresponding to the pedigree to which he or she belongs 2 assigns the size of the pedigree and the generational position of that individual in the pedigree founders are assigned to Generation 0 with numbers increasing through more recent generations and 3 assigns to each individual a number designating the founder of his or her paternal or maternal ancestral lineage The file containing data to be analyzed may be a Master File or any pedigree file consisting of records each of which contains a
420. t SIRE PID not deleted lt sire gt listed as DAM of KID1 lt kidl gt in MF 63 lt ego gt SIRE PID not changed lt dam gt listed as SIRE of KID1 lt kid1 gt in MF 64 E 65 66 lt ego gt SIRE PID not changed lt ego gt cannot be own parent lt ego gt DAM PID not deleted lt ego gt cannot be own parent where lt sire gt and lt dam gt are PIDs of EGO s parents and lt kid1 gt is the PID of the first offspring of the parent all as listed in the Master File These errors occur only when making changes to a record previously entered in the Master File Probable causes are a incorrect assignment of parental PID to EGO in the Master File b incorrect assignment of parental PID to lt kid1 gt in the Master File or c incorrect assignment of SEX to parent of EGO or lt kid1 gt as given in the Master File To correct these errors If a re assign correct parental PID to EGO in Master File If b first reassign correct parental PID to lt kid1 gt in Master File then re enter change of parental PID for EGO If c first re assign SEX of appropriate parent then re enter change of parental PID for EGO In all cases use ALTMASTR in ALTER mode and re run SETMASTR using the most recent Update and Master files see note on renaming and deleting these files Run INDEX after all changes have been made successfully Group 7 Birth Date changes A change in birth date may change the order
421. t 22 8 11 IF gt 13 75 Enter H for explanation shortcuts examples RETURN alone to continue to next step Last entry IF 161 gt 16 M This example shows an entry sequence required to make changes to SEX coding independently of val ues found in other items on the record conversion from M F and U to 1 2 and 3 respectively Item 16 has been marked with an asterisk indicating that at least one Conversion Table entry has been made for SEX The most recent of these specifying the change from F to 2 is shown in the line labeled Last entry just above the five command lines at the bottom of the screen display Entries have been made in the command sequence that will specify the change of M to 1 These will be transferred to the Last entry line when entry of this conversion is done as can be seen below 29 2 e NEWITEM April 19 1999 SI DAM S SE FIRST OFFSPRING SEQ 12 RE S S NE EGO SEQUENTIAL ID 9 10 deli XT PATERNAL SIB SI 13 XT MATERNAL SIB SI 14 XT FULL SI B SEQ 15 I oO UO amp NN OH N NE N ER OF OFFSPRING 16 PATERNAL SIBSHIP SIZ IATERNAL SIBSHIP SIZ FULL SIBSHIP SIZI EGO Permanent ID Birth Date YYYYMMDD Sire s Permanent ID Dam s Permanent ID Sex M F or U Da Co s te YYYYMMDD de Perman
422. t ID 8 Tot Ser Cholesterol Sex M F or U 9 APOAI Level PEDIGREE NUMBER 10 Discrete Trait TRANSLAT Ego Affection Status RANSTEST XMP Enter number corresponding to Ego Affection Status If item does exist enter C to create field and continue gt If an item representing Affection Status has not been designated previously a field is created containing the value 0 and added to the output record Next genetic loci are selected EGO Permanent ID 6 ADA Phenotype LT ENTIAL ID Sire s Permanent ID 7 APOB Pvu2a Genotype 12 EO Dam s Permanent ID 8 Tot Ser Cholesterol 13 Sex M F or U 9 APOAI Level 14 STATUS PEDIGREE NUMBER 10 Discrete Trait TRANSLAT Select locus RANSTEST XMP Enter numbers corresponding to items containing loci for inclusion in output Enter C to continue to next step gt Here the ADA and APOB Pvu2a loci have been chosen Notes on LINKAGE format conversion e TRANSLAT converts genotype representation from PEDSYS to LINKAGE format where allele sym bols are replaced by integer values e PEDSYS sex codes are converted as needed to 1 and 2 corresponding to males and females respectively unknown parental PIDs are converted from blanks to a single numeric 0 e TRANSLAT adds a leading X to Permanent IDs Data Type C if their first character is numeric e
423. t be specified in the command line with a leading S that is also as 10 The same problem may occur if PIDs begin with command characters P or p the page command April 19 1999 SHOW e 40 7 To circumvent this possibility the following alternates may be used lt n gt maybe substituted for S lt n gt or s lt n gt lt n gt de P lt n gt or p lt n gt For example specification of Sequential ID 10 would be 10 to distinguish it from PID S10 Likewise page 2 may be selected by entering 2 to distinguish it from ID P2 Characters entered at the console are first assumed to constitute a PID so that IDs beginning with S or P for example will always be found and displayed The entry is interpreted as a control sequence only if no corresponding PID is found in the file The alternates are available in all relevant PEDSYS programs e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example show subset out Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file show lt n gt out may be used as input to program SHOW Output Console screen and with the W write to file command show lt n gt out where lt n gt is the order in which alternate files are written Program limits Only five linked files may be selected for sequential display The Find function relatio
424. t date that contains only year Uninterpretable dates are written with a message to the error log file dates err The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example dates subset out Files Input Any Master File or Data File and an associated Code File Recursive use of output files is permitted that is file dates out may be used as input to program DATE Output dates out contains all records of the input file in their original order with specified date fields changed according to format codes New dates replace those selected for conversion except where constants are added to or subtracted from the original in which case new dates are appended as an item at the end of the record dates cde defines the record structure of dates out dates err contains information about records in which dates cannot be re formatted Program limits Formats of 40 different dates be changed 14 6 DATES July 7 1999 DBFILER Program DBFILER is used to create and modify the Directory File DBFILES making it possible to add or remove Master Files Data Files and sub directories from a database Changes are made only to DBFILES resident in the current parent directory and to DBFILES resident in sub directories resident in the parent directory Introductory Display DBFILER responds somewhat differently depending upon the prior existence of copies of th
425. t i lt Enter the Data Type of the item C I or R or S to skip gt SEQ lt Enter a single mnemonic for this item The current Item Number is displayed just below the input record display This is followed by a request for the number of characters in the record that are to be assigned to the item starting with the first unassigned character At this point the unassigned portion starts at the beginning of the record and it can be seen that the first non blank character in the record 1 is five spaces from this point This suggests that the first item is a five character integer which would be a reasonable guess even without prior knowledge of the record format Hence 5 characters have been assigned to this item In the next command its Data Type is set at i Entry of s here defines the item as one to be skipped when writing output records to file itemize out Finally the mnemonic SEQ is assigned to the new item When the mnemonic has been entered the full command display appears ER XMP Record 1 of 32 Length 95 e e e e EA EE A elesse O 0ID06119720309 M199804 repine lists 201ID04 Enter ASSIGN next item I to INSERT new Item SUBDIVIDE Item D to DELETE numbered item change MNEMONIC T to change Data TYPE change WIDTH of Item R to display an alternate R SAVE and EXIT April 20 1999 ITEMIZE e 24 3 Here the first item has been defined at the left most side o
426. t listed as parent of KID1 lt kidl gt in MF 52 where lt parntyp gt is the type i e SIRE or DAM of EGO s parent and lt kid1 gt is the PID of this parent s first offspring all as given in the Master File These errors occur only when making changes to a record previously entered in the Master File Probable causes are a incorrect keyboard entry of EGO PID or SEX or b incorrect assignment of parental PID to EGO or lt kid1 gt in the Master File To correct these errors If a re enter correct EGO PID or SEX If b first re assign parental PID of EGO or lt kid1 gt in Master File then re enter change of EGO s SEX In either case use ALTMASTR in ALTER mode and re run SETMASTR using the most recent Update and Master files see note on renaming and deleting these files Group 6 Incorrect parental assignment Parental PIDs cannot be deleted or changed if a the parent does not list EGO as an offspring in the Master File or b the parent type i e SIRE or DAM assumed for the new entry is not consistent with the parent type as found in the Master File If these conditions are found by cross checking PIDs of April 20 1999 SETMASTR 39 5 family members in the Master File the following errors may be reported lt ego gt SIRE PID not deleted EGO not found as offspring of lt sire gt in 61 lt ego gt DAM PID not deleted EGO not found as offspring of lt dam gt in MF 62 lt ego g
427. t may change as new programs are added or removed in the course of PEDSYS development with of age alterdat altmastr ancestor append browse calc code combine countped datalink dates dbfiler delrecs downcode duplic exclude foundrep fprint fprnen genefreq genomap index infer itemize kinship list makeped merge nenscript newitem nucfam pedsys pedtrim peelseq prepdraw reformat report segcheck setdata setmastr setpath show showdata sort subset tally translat triplets verifier Files fprint and nenscript generate Unix printer commands from program output File setpath con tains a program that controls file access pathways and is described in Chapter III Setting Directories and Running Pedsys Programs c PEDSYS Data Directories PEDSYS Master Files and Data Files are kept separately from PEDSYS programs in their own independent Data Directories Usually although not necessarily only one Master File is kept in a Data Directory The example Data Directory contains the following entries E XI DBFILES DPOINT XMP LOCUS MASTER XI ME T XM PE ES RANS EST xX EIGHTS CDE EIGHTS XMP PE ES examped tab A copy of the PEDSYS Directory File DBFILES is also included in each Data Directory DBFILES
428. t n gt Entry of or followed by an integer displays records belonging to the individual lt n gt records from the last one selected for display FilePos The default value of lt n gt is 1 so that entry of alone advances the display by one record Horizontal position remains unchanged Important note Entry of the command while displaying records in a Linked Multiple entry file will result in the display of records for an apparently unpredictable individual This is because the record counter is set at the record of the individual selected for display FilePos and the command operates by incrementing the record counter FilePos lt n gt Since ordering of records in Linked Multiple entry Data Files may be unpredictable so too may be the next individual shown RETURN Entry of RETURN alone advances the display to the record immediately following the last record currently displayed Again owing to the unpredictable order of records in Linked Multiple entry Data Files repeated entry of RETURN results in an unpredictable sequence of individuals shown This command makes it possible to switch the SHOWDATA record display rapidly between linked files selected when the program is started Entry of an asterisk switches the display cyclically to the next of the selected files here file HEMOGLOB XMP EMOGLOB XMP ID ID042 Items 4 Recs 13 LIFO Page 1 1 FilePos 31 238 1 2 3 4 EGO DATE hgb 30 29 28 27
429. t output items File QUANTGEN XMP Note Permanent and Sequential IDs from the Master File will be automatically added to output records Enter numbers corresponding to additional items to be included on output records Enter A to select all C to continue gt July 8 1999 PEDTRIM e 32 1 Since this is a Linked Data File pedigree information required by PEDTRIM are taken automatic ally from the Example Master File to which it is linked Note In order to include items from the Master File in PEDTRIM the Master File itself must be chosen explicitly from the File Selection Display above not done in this example b An unlinked file containing genotypic or phenotypic data It is often convenient to organize multiple genotypes and or phenotypes on the same record An example of this organization is given by file PEDTRTEST XMP in which genotypes for five loci have been assembled on records for each individual display from program BROWSE Top record 1 32 4 5 6 APOB CAI G6PD Pvu2a PHENO PHENO B A A B A A B D D HH H HHHHHKHHKHKKKHKHKHKHKHHKHE HHHW w When an unlinked file has been selected PEDTRIM compares its Code File with entries in CODE STD for standard mnemonics identifying Ego and Ego s parents As in the example shown above if the Code File does not contain mnemonics for Permanent IDs FA or SIRE and MO or DAM and or Sequential IDs SEQ
430. t rules for loci not in a map file April 20 1999 GENEFREO e 20 5 1 genefreq tab An example ot output file genefreq tab is shown below Phenotype Inferred types included N Typed Q O Gi D et Inferred types 32 27 included UNT BLANKS INFERRED UNINTERP OOU O H APOB Pvu2a G N Typed Genotype AUCD Inferred types 32 27 included A1A1 A1A2 A2A2 UNT BLANKS INFERRE UNINTE N Typed Pheno Inferred types 30 included A AB B G6PD PHENO TYPE N Typed XLCD Inferred types 20 6 GENEFREQ 32 26 included April 20 1999 The first line of each segment of the table is a header describing columns below it Mode of inheritance is shown in parentheses in the first column as is a note to the effect that inferred alleles have been included in frequency calculations Symbols and numbers of phenotypes found in the input file are shown in the Phenotype and Count columns respectively Below these are four categories with counts that are not actually included in computations UNT This is a reserved phenotypic symbol that indicates phenotypes that are permanently untestable usually because the individual or its blood or tissue sample is no longer available BLANKS Following the usual PEDSYS conven
431. t specifying prior calculations 1 Calculating simple functions addition of numerical sequences Choice 1 specifying simple calculations results in the following display April 19 1999 CALC e 9 1 EGO SEQUENTIAL ID 9 PATERNAL SIBSHIP SIZ 171 Date YYYYMMDD SIRE S SEO 10 MATERNAL SIBSHIP SIZ 18 1 Code DAM S SEQ 11 FULL SIBSHIP SIZE 19 s Permanent ID FIRST OFFSPRING SEQ 12 EGO Permanent ID 20 PEDIGREE NUMBER NE PATERNAL SIB SE 13 Birth Date YYYYMMDD 21 GENERATION NU MATERNAL SIB SE 14 Sire s Permanent ID X22 BSZ FSIBSZ FULL SIB SEQ 15 Dam s Permanent ID ER OF OFFSPRING 16 Sex M F or U 1 2 3 4 5 6 7 8 CALC Simple calculations sequences File MASTER XI Enter first operand from the list above or a constant preceded by K operator E then a second operand Precede operand with Log or LN for logs U for SI Unit conversion Enter R for random fractions S for integer sequence H for help C to continue to next step gt 10 11 lt COMMAND Commands Operators and E A first operand is selected by entering a number corresponding to a numerical value from the list of items above or a constant a number preceded by a k Immediately follow this operand with an operator and follow the operator by a second operand selecte
432. t the program The Q command terminates the program at which time the following summary display appears Interactive Mode Update Summary for QUANTGEN XMP File Records Modified 0 Added 0 Deleted 1 ETURN to continue Upon entry of RETURN the final screen display appears PA A AAA KKK KKK KKK KKK KK KKK AAA AE AE KKK KKK KKK KK KKK KK KKK KKK KKK KKK KKK AAA AAA AAA KKK KKK ALTERDAT is finished To complete the process of changing QUANTGEN XMP it will be necessary to run the program DELRECS A log of this session s updates can be found in alterdat log Output is in directory h1 population bdyke example32 QUANTGEN DEL Be sure to rename output files before rerunning this program F FF F F F HF F F FF FF F F F HF F KKK KKK KK KK KK KK KKK KR KR KKK KKK KKK KKK KKK KK KKK KKK KK KKK KKK KK KKK KKK KKK KKK KKK KKK KKK KK KKK Here a record was deleted so a reminder is given to run program DELRECS to complete the deletion process however other notices may be be included in this display If a new Linked Data File has been created a reminder to run program DATALINK appears if ALTERDAT was run in Batch Mode a reminder is given to run program SETDATA to add changes to the Data File 4 8 e ALTERDAT April 20 1999 Linked Multiple entry Data Files If the file to be modified is identified as a linked Multiple entry Data File commands governing th
433. t this point the PID of a new individual may be entered and another edit cycle begun Entry of RETURN alone redisplays the options display Updating QUANTGI Interactive Mode Enter E to EDIT records A to ADD records R to RESELECT items to be updated D to DELETE records Edit control O to set Order of access Order is RANDOM F to set conFirmation display Confirmation is ON L to switch Log setting LOG is ON If finished with QUANTGEN XMP C to CHANGE an existing file N to start a NEW file Q to QUIT program Note here that an additional command R appears in the first group of options This command makes it possible to reselect items for modification in subsequent records If a record for EGO cannot be found the following display appears WARNING No record in Data File for IDO77 Add a record for this individual Y N gt ALTERDAT automatically switches from EDIT to ADD mode if Y is selected Otherwise a request for a PID reappears followed by an EDIT display etc Command A Add new records to a Linked Single entry Data File The ADD procedure is very similar to EDIT except that ALTERDAT will not permit addition of records with IDs that duplicate those already in a Single entry Data File this restriction does not apply to Multiple entry files 4 4 e ALTERDAT April 20 1999 Command D Delete records from a Linked Single entry Data File A
434. t without saving and go on to the next record With confirmation OFF redisplay is suppressed and RETURN alone saves the record when editing is done command S is re quired to save the record when Confirmation is ON The default ON state is renewed each time a new file is selected for modification Command L Set the Log Interactive Mode only Entry of an L at the command line toggles the generation of an optional file that preserves a record of all operations performed during the current interactive ALTERDAT session This feature is not 4 6 e ALTERDAT April 20 1999 needed in Batch Mode since the update file lt FILENAME gt UPD serves the same purpose The default ON OFF status of this feature is set with the Log variable in the Data File Descriptor Record see note p in the Notes on DBFILES Record Formats section in Appendix A a The next three commands determine the course of action to be taken once modification of the current file has been completed Command C Change to another file for modification Entry of C here results in the following display which gives a brief summary of actions taken during the current session Update Summary for QUANTGEN XMP File 1 Records Modified 1 Added 0 Deleted 0 Press RETURN to continue gt This is followed by a return to the file selection display Command N Create a new Linked Single entry Data File Entry of N produces the update summary display shown above fo
435. te YYYYMMDD ENERATION NU Sire s Permanent I Exit Code Dam s Permanent ID ate s Permanent ID TRIPLETS Select Proband ID File subset out Enter a number above corresponding to Proband ID or C to continue to next step gt Here the pedigrees of the mates of individuals found in file subset out have been specified The program next proceeds to construct triplets Notes e Data from only the most recently entered record will be included in output if a Multiple entry Data File has been selected for input to TRIPLETS e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example triplets subset out Files Input Pedigree Information Master File pedigree contained in Data File itself or an unlinked pedigree file containing EGO PIDs that also appear in Data File Data File Linked Data File or unlinked Data File Probands Master File Data File or console keyboard Output triplets out contains one or more pedigrees connecting probands to their relatives according to limits specified on input triplets cde defines the record structure of triplets out Fa 46 4 TRIPLETS June 5 1999 VERIFIER Program VERIFIER checks any PEDSYS Master File or Data File for illegal data characters and values that are inconsistent with Code File definitions Introductory D VERIFIE
436. tems for a merge to occur The maximum field width of the Key Item is 99 characters The maximum number of records that may be merged is 60 000 for Unix and the Macintosh 8 000 for MS DOS a 28 6 MERGE April 19 1999 NEWITEM Program NEWITEM makes changes in selected items of data records as specified in a conversion table Changes in one item may be specified so that they are either independent of or dependent on values found in other items on the same record A previously created table may be used or a new table may be entered from the keyboard Introductory Display EDSYS program NEWITEM Copyright 1995 1999 SFBR NEWITEM makes changes in selected items of data records as specified in a conversion table Unlinked File EXAI PLE LOCUS Sub directory number file name or Q to quit When the Master File or Data File containing items to be converted has been selected the follow ing display appears Existing items may be changed and or new items may be created and added to th nd of each record Enter N to create new items or RETURN to continue without creating new items gt n If one or more items is to be created the following sequence appears once for each new item Enter item to right of pointer gt enter RETURN to advance cursor or to abort and re enter item Enter RETURN at first position when done gt
437. tep 1 Create a Code File by running program CODE choosing Create Mode and skipping the Master Code File option CODE will request entry of optional labels mnemonics field lengths and data types When entry is finished the output file should be named lt filename gt cde where lt filename gt is the name chosen to identify the Data File Step 2 Run program ALTERDAT in START Mode entering the name of the Data File and its associated Code File when prompted These should be lt filename gt lt ext gt and lt filename gt cde respectively that is the same file name selected when renaming the Code File One item must be selected as a record identification field ALTERDAT creates a Data File interactively without an intermediate step Step 3 Run a spot check of records in lt filename gt lt ext gt using program BROWSE or SHOW If data on the records are not correct it may be necessary to make corrections as described above for Linked Data Files Fa Creating an unlinked Data File from Imported Computer readable Data The easiest way to create an PEDSYS unlinked Data File from a foreign data file is to run program ITEMIZE Run a spot check of records in itemize out using program BROWSE or SHOW paying particular attention to records at the beginning and the end of the file If data on the records are not correct it may be necessary to make corrections as described above for Linked Data Files Optionally program DBFILER may be
438. ter Pointer Files are named MPOINT lt EXT gt where lt EXT gt is an extension identifying the population For example MPOINT XMP is the name of the Example Master Pointer File distributed with the PEDSYS package 6 The Data Pointer File Although PEDSYS Master Files and Data Files are in most cases independent of one another it is often necessary to access information for the same individual but kept in separate files There are several ways to do this but the most flexible is to make sure that the Data Files are linked to the Master File through a Data Pointer File A Data Pointer File contains a record for each individual in the Master File This record is made up of a variable number of fields the first of which must be Ego s Sequential ID number followed by data pointers to records in Data Files that contain information about Ego one data pointer for each linked Data File The FORTRAN format of this record is lt n gt I5 where lt n gt is the number of linked Data Files plus 1 In the case of a Multiple entry Data File the data pointer identifies the record containing the last entry for Ego Previous entries can then be identified by means of the internal pointers described above If there is no entry for Ego in a Data File the data pointer will have a value of 0 Data Pointer Files are normally created with the PEDSYS program DATALINK A new field is added to all records in the Data Pointer File each time another Data File is linked
439. that are ancestors of subsets of the probands selected This is controlled in the display that appears next A list of individuals that are ancestral to at least lt n gt probands will be generated ancestor must have in order to be included in the list 2 3 gt 3 Enter lt n gt the minimum number of proband descendants that each The lower number of probands is always two while the upper bound is determined by the program s initial analysis Here it can be seen that the maximum number of probands sharing a common ancestor is three Choosing this number results in the following display 2 ancestors have been found that are common to at least 3 probands Ancestor No Pro Av No SEQ 12 4 April 20 1999 PID bands Steps ID065 2 00 ID042 3 00 Enter D to display a list of proband descendants of an ancestor above N to generate a list of ancestors for a new subset of probands S to save only proband and ancestor files P to create files containing PEDIGREES connecting ancestors to their descendants Enter Q to quit without saving gt d ANCESTOR 6 3 Command D Display a list of proband descendants of an ancestor Entry of this command produces the following display from which a single ancestor Sequential ID as specified earlier is selected 2 ancestors have been found that are common to at least 3 probands Ancestor No Pro Av No SEQ PID bands Steps 12 ID0
440. that identify Ego parents and SEX SEO SSEQ or FSEO DSEQ or MSEQ and SEX respectively a Standard Item List appears with instructions to select the unidentified items These must conform to format and content specifications described below Pedigree Draw does not require that gender be identified so that it is not absolutely necessary to select this item When selection of IDs has been done or if the Code File does contain the appropriate standard mnemonics the following display appears May 19 1999 TRANSLAT 45 3 EGO SE Q U ENTIAL ID SIRE S SE Q DAM S SI EO FIRST OFFSPRING SEQ EX PA ERNAL SIB SE 8 10 11 12 U ER OF OFFSPRING ERNAL SIBSHIP SIZ A ERNAL SIBSHIP SIZ FULI EGO EX MA ERNAL SIB SE EX FU LL SIB SEQ 13 14 Birth Date L SIBSHIP SIZE Permanent ID YYYYMMDD Sire s Permanent ID 15 KTG 17 18 Tg 20 21 Dam s Permanent ID Sex M F or U Exit Date YYYYMMDD t Code ate s Permanent ID PEDIGREE NUMBE GENERATION NU Exi TRANSLAT Select text fields File MASTER XMP Enter numbers corresponding to items to be included as optional text fields Required text items are pre selected All items are Enter C to continue 5 items maximum truncated if longer than 24 characte
441. that records for fictitious offspring also may be created when needed as described below Query 3 Create an offspring record for mated pairs without progeny Y N gt Some genetic analysis programs will not process individuals that have mated into a pedigree but do not have offspring listed in the pedigree file INDEX will create a fictitious offspring for pairs without progeny if the following conditions are met e PIDs for EGO FA and MO must be included in the input pedigree file SEX code is required e Records must include an item containing the Permanent ID of a mate The input Code File must contain an Item Descriptor Record with the code MATE or SPOUSE as the first and only mnemonic word e Any individual listed as a mate must also appear as Ego in the pedigree file Entry of y results in creation of a single fictitious offspring for each pair PIDs of newly created offspring are formed as described above for missing parents Query 4 Some genetic analysis programs interpret 0 as a legitimate pedigree number and thus misinterpret assignment of unrelated single individuals to this category This can be avoided by choosing option 2 below which assigns such individuals their own separate pedigree numbers 22 2 e INDEX April 19 1999 Assign individuals that have neither parents nor offspring 1 All to the same pedigr Pedigr 0 2 Each to a separate pedigr Enter number corresponding to choice Cre
442. the Master File is selected Error Messages A number of conditions force DATALINK to terminate without establishing links between files When any of these occurs a message is written to file datalink err These messages are as follows ERROR No Data Files to link to MASTER lt EXT gt This error is most likely to occur when no Data File information has been entered in the Directory File DBFILES It can also occur if the filename extension lt EXT gt on a Data File to be linked has been left blank or does not match the extension found in DBFILES To correct the error make sure that all necessary information about the Data File has been entered in DBFILES see chapter describing pro gram DBFILER and that this information is consistent with the name and extension of the Data File ERROR More than 50 Data Files This error occurs when the PEDSYS limit of 50 Linked Data Files per Master File is exceeded To correct this error one or more Data Files will have to be removed from DBFILES ERROR Master File and Data Files must have valid extensions This error occurs when attempting to create a linked database without using a filename extension lt EXT gt that is the extension is missing from DBFILES and from Master File and Data Files To correct the error make sure that all necessary information about the Master File and Data File has been entered in DBFILES see chapter describing program DBFILER and that nam
443. the first program used in a two step process required to make changes in Master Files from keyboard data entry Introductory Display EDSYS program ALTMASTR Copyright 1992 1999 SFBR ALTMASTR is an editing program for Master File records Changes made with this program are kept in one or more temporary Update Files used in turn as input to SETMASTR and or DELRECS programs that incorporate them permanently into the original Master File ote An appropriate Master Code File must be available to this program Enter C to make CHANGES to an existing Master File S to START new Master File Q to QUIT program Changing an existing Master File When choice C for CHANGES is selected a Standard File List Display showing only Master Files appears Example Master File Enter the number corresponding to the file to change gt 1 If passwords have been included in the Master File Descriptor Record of DBFILES see note h in the Notes on DBFILES Record Formats section in Appendix A a request for entry of a password will appear on the screen When a correct password is entered or if no password is required the following display is shown Enter E to EDIT Master File records A to ADD new records to Master File D to DELETE records from Master File X to EXIT program Command E Edit Master File records Entering E EDIT results in a Standard Item List
444. ther point in the display above opportunities for selecting a different set of items for the parents would have been given The files from which these items may be selected are limited to those selected initially Next the following display appears from which individual probands that define the triplets are selected Pedigrees may be constructed for probands entered from 1 Keyboard 2 Unlinked File 3 EXAMPLE 4 LOCUS Sub directory Enter number above corresponding to the appropriate source of proband IDs gt 1 Source 1 Proband IDs entered from the keyboard Choice 1 shown above specifies that proband IDs are to be entered from the keyboard When IDs have been extracted from a Master File the form of the IDs Permanent or Sequential must be specified before keyboard entry begins Enter P if probands are identified by Permanent IDs S if probands are identified by Sequential IDs gt S Here Sequential IDs have been selected June 5 1999 TRIPLETS 46 3 Source 2 3 or4 Proband IDs read from a Proband Input File A proband file is often a subset of the input pedigree file typically a Master File but may be any Data File whose records contain IDs in the appropriate form that is Permanent or Sequential Selection of a single item containing the proband ID is made from a Standard Item List Display EGO Permanent ID Sex M F or U EDIGREE NUMBE Birth Date YYYYM Exit Da
445. though the default is random order the most convenient order depends on the number and regularity of changes to be made April 20 1999 ALTERDAT e 4 5 RANDOM Order When items to be changed occur in a sporadic pattern for example when errors in a small number of records require correction a random order of access may be preferable Each field to be changed or added is represented as a line on the screen consisting of a numbered item label followed by data space marked off by angle brackets Each time an item is to be edited its number is entered and the item modified When editing is finished a request for another ID is given Example displays above are all set to Random Order SEQUENTIAL Order On the other hand when a fixed set of items is to be changed repeatedly typically when new records are being entered into the file entry of data items in sequential order is likely to require the fewest keystrokes Each field to be changed or added is represented as a line on the screen consisting of an numbered item label followed by data space marked off by angle brackets The cursor moves automatically to a new line when entry of values for each item is completed Entry of RETURN as the initial character of any field leaves the current value unchanged important in the carry over feature entry of a single blank as the initial character will erase the entire field When all items have been completed or if the character right square brack
446. three digit representation of the year implies a third millenium date i e 001 2001 Two digit representation of year YYMMDD or YY alone is not allowed e A date entered from the keyboard must have the same length as is specified in the Code File For example when dates are specified as having length 8 it will be necessary to enter D followed by exactly 8 digits whose order corresponds to YYYYMMDD An error message is displayed on the screen if the length is not correct e At least one of the dates for an age calculation must be taken from the individual s record that is it must be selected from the item list display Items that are not defined as dates in the Code File that is data type D cannot be used in age calculations An error message will be displayed on the screen if this requirement is not met e In contrast to other PEDSYS data types representation of unknown or missing dates depends to some extent on context This is because a blank date field may designate not only dates that are unknown or missing in the usual sense but also anticipated dates of events that have not yet occurred such as deaths or scheduled examinations etc In some cases events may be known to have occurred but evidence for associated dates may not be implicit in the database For example it may be known that an individual has died or has been examined in clinic but no information about the event is available or recorded In this case t
447. ting Master File always requires an up to date Master Pointer File if new records are to be added to a Master File that is already linked to one or more Data Files an up to date Data Pointer File is also required When this command is given the following display appears Example Master File gt 1 MASTER XMP w Enter the number corresponding to the file to change ill be updated but the file as it was before changes were mad will be sav d under the name MASTER OLD File UPDATE XMP will be renamed UPDATE OLD Enter C to continue O to quit without updating file gt Upon entry of c the program begins execution April 20 1999 SETMASTR 39 1 S Starting a new Master File Starting a new Master File from information stored in UPDATE lt EXT gt with SETMASTR uses some of the same procedures as program DBFILER That is it will create and configure a Directory File DBFILES if one does not already exist This commands results in the following display File UPDATE lt ext gt will be used to create a new MASTER lt ext gt where lt ext gt is a three character file extension used as a population identifier gt DOG lt Enter the identifier for this population IASTER DOG will be created and file UPDATE DOG will be renamed UPDAT Enter C to continue Q to quit without creating file gt DBFILES has been created Assign individuals that
448. tion Program INFER produces an Error File of this kind c Log Files In many File Management Programs it is useful to keep an account of changes and updates made to individual records These changes are saved in an output text file which has the extension log consisting of records bearing a message of varying length and format No accompanying Code File is provided PEDSYS programs that produce Log Files of this sort are ALTERDAT DELRECS INFER and SETMASTR d Tabular Output Files A few programs compute summary statistics from population or family data Output from these programs has a tabular format which is saved without an accompanying Code File in an output file having the extension tab PEDSYS programs that produce Tabular Output Files are ANCESTOR CODE GENCHECK GENEFREQ LIST NEWITEM PREPDRAW SEGCHECK TALLY and TRANSLAT e Miscellaneous Output Files Some PEDSYS programs produce special purpose output files in addition to standard cde out err and log files Program INDEX produces a file named index mpt which when renamed becomes a Master Pointer File Program ALTERDAT produces files named lt filename gt UPD and lt filename gt DEL that are used in turn as input to programs SETDATA and DELRECS respectively The ALTERDAT SETDATA program sequence is used to update records and the ALTERDAT DELRECS sequence is used to delete records from Data Files Program ALTMASTR produces two output files named UPDAT
449. tion blank fields represent missing data INFERRED This is simply an enumeration of the inferred phenotypes found in the input file and has no bearing on whether or not inferred types are included in frequency calculations UNINTERP This is an error category which is incremented whenever a phenotypic symbol is a not found in the Phenotype Genotype Map File or b does not follow the rules described above for autosomal codominant loci 2 genefreq out An example ot output file genefreq out is shown below Pa PRO SO e e e RS UT I o o OOp pm OOOoOOO The first four items on records in this file consist of mnemonics identifying the locus in question These are followed by an allele descriptor and the frequency of that allele There is a separate record for each allele Fi Files Input A Data File having records containing genotypic or phenotypic data and an associated Code File Optionally a Phenotype Genotype Map File April 20 1999 GENEFREO e 20 7 Output genefreq tab contains summary tabulations of gene and genotype or phenotype frequencies for each locus selected genefreq err contains messages about incorrectly formulated symbols Algorithm R Polich L Freeman Shade Fa 20 8 GENEFREQ April 20 1999 GENOMAP Program GENOMAP is used to create and or edit Genotype Phenotype Map Tables required to spe cif
450. tly to the request for a starting record number For example entry of f 8 eq 2 at the command line is equivalent to the sequence described above Subsequent records containing the same value can be found by entering F again etc The message End of search appears when the value sought is not found in subsequent records in the file The message will also appear if the value is not found at all in the file A substring feature permits a search for a sequence of characters enclosed in quotes that occurs at any position in the field occupied by the item For example the substring 1985 would search for all occurrences of the year regardless of the month or day included in the date field Notes e Partial items are not displayed This means that it may not be possible to view items that exceed the width of the unlocked portion of the window e When a PID or SEQ is entered for a Multiple entry Data File the most recently entered record for the individual chosen is displayed as the first line on the screen To see other records for that individual use the command with the number found in the last item of the record This is the internal pointer to the next most recently entered record e Alternates are provided for the leading command characters specifying Sequential ID Item and page numbers This is because there is the possibility of conflict between the defaults and PIDs that may begin with the same characters For example suppose a Master File
451. to Pedigree Draw 5 0 format The program auto matically selects required items PIDs and SEX and allows choice of text fields from PEDSYS records Codes designating Pedigree Draw symbol types and attributes may selected from four symbol palettes Application of symbol codes is conditional upon values found in specified items on the PEDSYS input record The file containing data to be converted to Pedigree Draw format may be a Master File alone a Master File with one or more Linked Data Files or any pedigree file consisting of records each of which contains minimally a unique identifier for EGO Father and Mother Introductory Display EDSYS program PREPDRAW Copyright 1996 1999 SFBR EPDRAW converts PEDSYS pedigree records to Pedigree Draw 5 0 format Unlinked File 2 EXAI PLE da LOCUS Sub directory Enter number file name or Q to quit gt 2 When a PEDSYS Data Directory such as the EXAMPLE Directory shown above the following dis play appears Example Master File arkers Quant P types Blood Sample Inventory Hemoglobin Levels Data may be selected from one or more linked files Enter numbers corres ponding to files s above or RETURN to continue gt 2 Note that the Example Master File has been pre selected and that information from one or more Linked Data Files may be chosen for inclusion in output The option of assembling data from multiple files is not given if
452. to choice gt 2 Here two PIDs have been entered and a choice has been made to skip records of any individuals with inbreeding coefficients of zero that is they not written to the output file 2 Proband IDs read from a file A proband file is often a subset of the input pedigree file typically a Master File but may be any Data File whose records contain IDs in the appropriate form that is Permanent or Sequential Selection of a single item containing the proband ID is made from a Standard Item List Display EGO Permanent ID Sex M F or U EDIGREE NUMB Birth Date YYYYM Exit Date YYYYMMDD ENERATION NUI Sire s Permanent I Exit Code Dam s Permanent ID ate s Permanent ID Identify PROBAND File examped KINSHIP Enter a number above corresponding to Proband ID or C to continue to next step gt 8 25 2 KINSHIP April 20 1999 Here inbreeding coefficients of individuals identified by PIDs as mates have been specified Cal culations will be done for mates found on all records of file examped so Calculating kinship coefficients Coefficients of kinship are calculated between pairs of individuals when choice 2 or 4 is selected in the command line of the Introductory Display The source of these pairs is controlled in the next dis play Calculate kinship between pairs of individuals Both members of which are selected from the same file
453. ts Lost enumerates triplets that would no longer be informative for the locus selected if the particular downcoding equivalence is chosen e Heterozygotes Lost enumerates heterozygous genotypes that would be changed to homozygotes if April 19 1999 DOWNCODE 17 3 the particular equivalence is chosen e Nuc Fams Affected enumerates the families in which some loss of information would result if the particular equivalence is chosen Usually less information is sacrificed when rare alleles are eliminated and as a convenience changes are listed in the table in order of increasing loss of information In this example the default change 1 will eliminate rare allele C by changing it to allele F From the table above it can be seen that changes 1 through 4 will result in no loss of informative triplets or heterozygotes in any family and so any of these is a good candidate for downcoding For this example we have chosen change 1 which produces the following result D2S1329 Genotypes Current Start Alleles 5 6 Informative triplets 13 13 Allele Equivalence Triplets Heterozygotes Nuc Fams Lost Lost Affected 0 1 0 to to to to to to to to to to hange hange hange hange hange hange hange hange hange hange AR AA PoPruvt gt Q OQ OOO Ct Oy gt 4 4 amp amp 4 amp WNNNNEHEHHEH HE 5 0 N ON N amp M h w D NN EE HR HR HE ds 2 Sa 4 Da 6 da 8 di 0 hb
454. ucts the minimal pedigree linking ancestors to their proband descendants PORTANT The file from which the pedigr is generated must be an indexed pedigree file with an associated Master Pointer File Unlinked file age out Example Master File Enter the number of the pedigr file to use or Q to quit gt 1 ANCESTOR automatically identifies pedigree files by searching for standard mnemonics identify ing Ego Ego s parents and sex in the Code File of the Data File selected For example the Code File associated with age out choice 2 above has been found to contain these mnemonics and the Example Master File choice 3 is by definition a pedigree file Use of an unlinked pedigr file requires that the file be in Master File format that is it must be indexed and have associated with it a Code File and a Master Pointer File such as INDEX MPT Enter the name of the pedigr file to us gt age out Enter name of the Code File for index out or RETURN for age cde gt Enter the name of the Master Pointer File gt MPOINT XMP April 20 1999 ANCESTOR 6 1 Here the unlinked file category choice 1 and file age out have been selected this file could have been selected directly as choice 2 If a Master File has been selected its associated pointer file is auto matically used For an unlinked file to run successfully it too must contain these standard ped
455. ult in selection of an incorrect item if input consists of multiple files containing duplicate item names e Shortcuts A shortcut may be used to speed entry of PREPDRAW command sequences by reducing the number of separate command sequences required for testing a single item against multiple test values A single sequence may be written for this case as follows if 12 EQ IDO71 ID049 ID045 ID034 then symbol a that is multiple test values separated by commas may follow a single logical operator When the initial operator is EQ commas separating test values are interpreted as OR operators so that the statement above is true when Item 12 EGO PID is the same as any one of the PIDs in the list For any other initial operator commas separating test values are interpreted as AND operators Thus the following statement IF 8 LT 9 10 11 is true when Item 8 NUMBER OF OFFSPRING is less than all of the values of Items 9 10 and 11 on that record PATERNAL MATERNAL and FULL SIBSHIP SIZE respectively This shortcut applies only to test values that is multiple item numbers may not be tested in this way Data types of test items are determined by the data types listed in the input Code File The constant designator can also be used with multiple test values For example IF 11 eq k 1 2 3 IF 11 eq 9 k2 are legitimate expressions e Substring searches Substrings are defined by preceding or appending an asterisk to the c
456. ultiple entry Data File has been chosen the order that data records will appear within header groups in the output list may be selected from the following display April 19 1999 REPORT e 36 3 1 Most recently entered records first 2 Most recently entered records last Enter number corresponding to order that DATA records should appear in list gt The choice of order here assumes that records in the file remain in their original sequence that is determined by time of entry This order may be changed a by initially selecting the file from the Unlinked category in the File List Display when the program is first started and then sorting as described below Unlinked Data Files If an unlinked Data File is chosen to supply data records it will be necessary to designate the Permanent ID and to ensure that the file has been sorted with the major sort on this as the Key Item The example below shows the Item List for an unlinked file from which the Key Item is selected 1 ID 3 Weight 2 Sample Date 4 INTERNAL POINTER EPORT Select ID and sort items File WEIGHTS XMP Select items from the list above to be sorted in order of decreasing sig nificance First item selected MUST be a PID Key Item Precede item number with a D to sort in descending order Enter C to continue gt The first item selected here the major sort must be a PID Usually but not necessarily this will
457. umber or name gt Here any single locus may be selected by entering its corresponding file number 3 18 Command se quences that follow are the same as those outlined above for unlinked files in the main Data Directory sa 3 Multiple loci listed in a special purpose file in the LOCUS Sub directory Alternately a pre defined set of loci file numbers 1 and 2 may be chosen The content of file 1 AllLoci is shown below April 20 1999 GENEFREO e 20 3 APOBpvu2a CA1 ErrorDemo G6PD Note that the first record in the file must contain only the word FILELIST and that this record is followed by a list of file names exactly as they appear in the sub directory DBFILES In the example above we have included all locus files but the list may be constructed to include any subset as shown below Command sequences that follow are also the same as those outlined above for unlinked files in the main Data Directory A e Additional requirements for calculating X linked gene frequencies When an X linked is designated in the Genotype Phenotype Mapping File GENEFREQ compares the Code File of the input locus file with entries in CODE STD for standard mnemonics identifying Ego and Ego s parents If the Code File does not contain the mnemonic SEX a pedigree file containing this information along with Ego PIDs that match those in the input file must be selected G6PD PHENO TYPE is listed as an X linked
458. ust be entered from the following display Pedigrees may be constructed for 2 200 probands entered from Keyboard Unlinked File age out Example LOCUS Sub directory Enter number for the appropriate source of probands gt 1 Choice 1 Proband IDs entered from the keyboard Choice 1 shown above specifies that proband IDs are to be entered from the keyboard Before key board entry begins the form of the IDs Permanent or Sequential must be specified ANCESTOR identifies pedigrees by starting with a proband and accumulating his or her progenitors in ascending generations The upper generation must also be specified here 6 2 e ANCESTOR April 20 1999 Enter gt P P S if probands are identified by Permanent ID if by Sequential ID Enter the maximum number of ascending generations 1 20 relative to each proband to be included in the pedigree gt 3 In this example Permanent ID has been selected and maximum pedigree depth for each proband has been set at three generations which is sufficient to include ancestors in the earliest generation in the Example pedigree Next keyboard entry proceeds as follows gt ID067 lt gt ID071 lt gt ID049 lt gt ID069 lt gt lt ID ID ID ID ID Enter proband s Permanent ID RETURN alone terminates entry Ancestors of all probands selected initially have been found but it sometimes may be useful to speci fy individuals
459. ut field width for any item as the length of the longest string found in the corresponding field of the foreign input record including leading and trailing blanks except that input fields of null width designated by a pair of adjacent delimiter characters or a delimiter character followed directly by the end of record are assigned a single blank character item in PEDSYS format e In foreign to PEDSYS translation computed width can be increased if specified by an appropriate pre existing Code File accompanying the input file but it cannot be decreased this way e Output file translat cde will contain the same Item Labels as the pre existing Code File used to define PEDSYS output format if no field width Data Type or item number conflicts are found If conflicts are found translat cde defaults to generalized descriptors ITEM 1 ITEM 2 etc and a message is displayed when execution is finished e See Appendix B Program TRANSLAT Format Translations for more information on charac ter delimited formats 3 PEDSYS to Pedigree Draw 4 4 When PEDSYS to Pedigree Draw 4 4 Mamelka et al 1993 format translation is chosen Standard File List Displays appear from which the file to be translated is chosen The program compares the Code File of the file selected with entries in CODE STD for standard mnemonics identifying Ego and Ego s parents which are always present in a Master Code File If the Code File does not contain standard mnemonics
460. ution e File TRANSTEST XMP was created to illustrate conversions to input formats for pedigree analysis programs by combining items from records in MASTER XMP Items 1 5 and 11 13 and QUANTGEN XMP Items 6 9 and adding an item called Discrete Trait Item 10 Its Code File TRANSTEST CDE is shown below May 19 1999 TRANSLAT 45 5 Example for Program TRANSLAT 5 EGO Permanent ID Sire s Permanent ID Dam s Permanent ID Sex M F or U PEDIGREE NUMBER ADA Phenotype PHENO APOB Pvu2a Genotype Pvu2a Tot Ser Cholesterol APOAI Level APOAI Level Discrete Trait DISCRT TRAIT EGO SEQUENTIAL ID SI SIRE S SEQ SSI DAM S SEQ DSI EPER A A Er e OC O1 O1 O1 HO O1 Or UU 5 and 6 PEDSYS to FISHER and MENDEL formats If FISHER or MENDEL format has been selected TRANSLAT searches the input Code File for an item with the mnemonic TWIN a one character status flag a single blank character is inserted in output records if no twin status flag is found Program FISHER expects input of quantitative phenotypic data which are chosen from a standard Item Selection Display EGO Permanent ID 6 ADA Phenotype ENTIAL ID Sire s Permanent ID 7 APOB Pvu2a Genotype Dam s Permanent ID 8 Tot Ser Cholesterol Sex M F or U 9 APOAI Level PEDIGREE NUMBER 10 Discrete Trait RANSTEST XMP TRANSLAT S
461. ver page of listings produced by the program LIST Here is an example of SUBIN TMP SUBINFO Subset constructed with the following commands INCLUDE SEX EQ lt 1 gt 0 pedsys example MASTER XMP To better illustrate the function of the number preceding the file name here is an example of SORTIN TMP that is produced after the file MASTER XMP has been processed by program SUBSET immediately prior to being sorted SORTINFO Records sorted in following order major sort first VARIABLE E SEX VARIABLE ANIMAL ID SUBINFO Subset constructed with the following commands INCLUDE SEX EQ lt 1 gt 1 pedsys example MASTER XMP SORTIN TMP now includes information from SUBIN TMP The 1 preceding the file name informs program LIST that an expanded processing history of MASTER XMP is to be printed on the cover page and page headings Occasionally when a program is interrupted or ends prematurely one or more temporary system files will not be erased Any tmp files remaining in the working directory may be deleted manually although this is usually unnecessary No attention need be paid to these files other than to understand their effects They are produced anew each time a program is run and are read automatically A 22 e APPENDIX A June 12 1999 15 The Data Path File Unless otherwise directed PEDSYS programs read data from and send their output to the current open Data Di
462. warning is given when item field length is increased as the result of conversion e Floating point numbers Data Type R are rounded when converted to integers Data Type I e The command line startup shortcut program name followed by a blank and an input file name may be used to start this program Example newitem subset out oe Conversion Table Format The Conversion Table begins with a group of records that define Data Items whose values a are to be changed or b are used to determine changes in other items The first field in these records consists of a sequential number three characters followed by four six character strings that are identical to mnemonic words of the appropriate Descriptor Record of the input Code File All fields are separated by a single blank These records are followed by a blank line which in turn is followed by records specifying changes to be made These records have a format identical to that found in the Last entry line shown in the command entry screen described above Shown below is the Conversion Table resulting from the changes specified in the examples shown above 29 8 e NEWITEM April 19 1999 KID SIBSZ EX KidSib Ratio SEX EQ E EX 1 SEX EQ E EX 2 SEX EQ F EX BLANKS FSIBSZ NE EN KidSib Ratio NKID FSIBSZ ELSE KidSib Ratio NKID Provision is made for reuse of the Conversion Table This is possible howev
463. when a new table is started from the key board choice S as is shown above Specifying critical data items using the table is a two step process Step 1 Marking Critical Data Items Critical data items are divided into two classes 1 Single independent items Missing or invalid data for any one of these items make Ego a candidate for removal from the pedigree These are designated by preceding item numbers with an equal sign when they are entered in the command line of the Item List Display These are marked with after selection 2 Grouped alternate items Missing or invalid data for some proportion of these items taken as a group make Ego a candidate for removal from the pedigree These items are designated by preceding item numbers with a plus sign at entry These are marked with after selection Critical data items are selected from the next Item List Display containing the items chosen previously for inclusion in output records 1 EGO Permanent ID 4 ABO Phenotype 7 CA1 Phenotype 2 Sire s Permanent ID 5 ADA Phenotype 8 G6PD Phenotype 3 Dam s Permanent ID 6 APOB Pvu2a Genotype EDTRIM Mark critical data Items above will be included on output records Precede numbers with for items that MUST contain valid data Precede numbers with to select a set of which a MINIMUM NUMBER must contain valid data Enter C to continue to next step gt July 8 1999 PEDTRIM e 32 3 In the example ab
464. which he has inherited from ID034 The iterative nature of the process is implied in the case of individual ID067 whose genotype BC could not be inferred completely until her father s genotype BB had been determined Note that in this pedigree it has not been possible to infer the phenotype of individual ID056 However since his offspring ID047 is a BB homozygote we can infer that ID056 has at least one B allele as is indicated by the symbol enclosed in parentheses The other allele is unknown however and is represented by a dash 23 6 e INFER April 20 1999 Example 2 Inferring Dominant Recessive Phenotypes ABO locus A Phenotype Genotype Map is required for correct inferences to be made for phenotypes that show dominance If the selected phenotype is included in this file INFER proceeds in the same fashion as it does when making inferences from codominant phenotypes In the example that follows the ABO Phenotype has been selected INFER proceeds by assigning genotypes on an a priori basis as illustrated in the diagram below Q E ID070 1D054 AB A ab a Pedigree DrAw Directly below each individual s PID is shown the ABO phenotype exactly as it appears in the ABO locus file Note that there is no entry for individuals ID045 or ID062 Below each phenotype is an a priori genotype assignment recessive homozygotes ab and oo can be deduced unambiguously from phenotypes AB and O respectively and the presence of at le
465. wing message RA KKK KK KKK KKK KKK KKK KKK KKK KKK AE AE AE KKK KKK KKK KKK KKK KKK KKK KKK KKK AAA KKK KKK KKK KKK KK A PEELSEQ is finished Output is in directory export home population bdyke example32 peelseg tab The maximum cutset size is 2 Be sure to rename output files before rerunning this program K peelseq2 tab RA A KKK KKK KK KK KKK KKK KKK KKK KKK KKK AE AE AAA KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK Notes e IDs appearing in output file peelseq tab refer only to the indexed pedigree file used as input to PEELSEQ Thus these IDs may not correspond to Sequential IDs in the population Master File e Output file peelseq2 tab is not produced if the input Code File does not contain standard mnemonics for PIDs Files Input Any Master File or indexed pedigree file with an accompanying Code File Output peelseq tab contains the peeling sequence with integer IDs formatted for input to PAP peelseq2 tab contains a more easily interpretable version of the peeling sequence with Per manent IDs This file is not used as input to PAP April 22 1999 PEELSEQ 33 3 Algorithm J W MacCluer D T Bishop Reference Cannings C Thompson EA and Skolnick MH 1978 Probability functions on complex pedigrees Advances in Applied Probability 10 26 61 Fa 33 4 e PEELSEQ April 22 1999 PREPDRAW Program PREPDRAW changes PEDSYS records in
466. wn above ADA APOAT EGO EXCODE TSC PHENO Level TYPE ette 1 EXCODE EGO EQ ette 2 Pal IF IF Pal Standard pre defined symbol types EQ 1 THEN SYMBOL Deceased ID015 THEN SYMBOL Proband Filled quadrants representing traits IF SC G KO AND TSC IF Pal TE Pal SC G ette 3 APOAI K99 T Two charac HEN SYMBOL K99 ter alp evel EQ KO HEN SYMBOL Trait 1 4 Trait 2 3 habetic codes HEN SY OL Asterisk tte 4 Miscellaneous pr defined attributes IF ADA PHENO TYPE EQ BLANKS THEN SYMBOL Gray fill Text lines 1 ADA PHENO 2 APOB Pvu2a TYPE GENO TYPE Files Input 1 A Master File with or without one or more linked Data Files and associated Code File s May 4 1999 PREPDRAW e 34 11 2 A pedigree file having records containing minimally a unique identifier for EGO and EGO s parents and associated Code File Output prepdraw ped contains a Pedigree Draw 5 0 header record followed by all records of the input file in the order they have been selected with specified items changed according to the Symbol Selection Table and palettes prepdraw tab contains a new or revised Symbol Selection Table This file is created each time a new table is generated or when a previously c
467. y 4 1999 Fe PREPDRAW e 34 7 Step 5 Selecting Individuals to be Included in Pedigree If one or more linked files has been used to define symbols and or text fields the edit display menu includes an additional command I to VIEW and EDIT text and symbol selections to IDENTIFY pedigree records for inclusion in output file to SAVE file prepdraw tab and EXIT program to QUIT program without executing or saving table Enter letter above corresponding to action to be taken gt i Command I results in a request for identification of records of individuals to be included in the output file prepdraw tab Output file prepdraw ped may contain all or a subset of individuals found in the input pedigree file Note Pedigree links may be lost if a subset is chosen Unlinked File EXAI PLE LOCUS Sub directory Enter number file name or Q to quit gt 2 When an appropriate pedigree file has been chosen the following display appears EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING 15 Dam s Permanent ID SIRE S S 9 PATERNAL SIBSHIP SIZ 16 Sex M F or U DAM S SE 10 MATERNAL SIBSHIP SIZ 17 Exit Date YYYYMMDD FIRST OFFSPRING SEQ 11 FULL SIBSHIP SIZI 18 Exit Code EXT PATERNAL SIB SI 12 EGO Permanent ID 19 Mate s Permanent ID EXT MATERNAL SIB SI 13 Birth Date YYYYMMDD 20 PEDIGREE NUMBE EXT FULL SIB SEQ 14 Sire s Permanent ID 21 GENERATION NU
468. y SEX column by row statistics for a Master file Enter C to continue to next step gt Here again a two way classification of NUMBER OF OFFSPRING by Sex has been selected Since the tabulated variable is numeric the following sequence appears after the Standard Confirmation and Editing step Set bounds on the value of NUMBER OF OFFSPRING for which Distribution Parameters are calculated Y N Y Enter INCLUSIVE lower bound for value of NUMBER OF OFFSPRING Values below this bound will not be tallied Enter RETURN alone to let smallest data value determine lower bound gt 1 Enter EXCLUSIVE upper bound for value of NUMBER OF OFFSPRING Values equal to or greater than this bound will not be tallied Enter RETURN alone to let highest data value determine upper bound gt 5 If N is entered in response to the first query the program will begin computing parameters for all values of the item selected In this example as well choice Y was made initially to set bounds on the tabulated variable which leads next to the options of setting its lower and upper bounds here 1 and 5 respectively Note the choice of grouping the tabulated variable into a reduced number of classes is not offered for the Distribution Parameters option Output Example Distribution Parameters Below is an display of file tally tab showing Distribution
469. y of choice E in the introductory screen results in the following display Enter name of Genotype Phenotype Map File to edit gt genomap tab When the name of the Genotype Phenotype Map File has been entered the following display ap pears genomap tab Genotype Phenotype Map File ADA PHENO TYPE ABO PHENO TYPE G6PD PHENO TYPE DYS391 PHENO TYPE Enter V to view locus E to edit locus A to add locus D to delete locus C to continue generating and saving output file gt 21 6 GENOMAP June 10 1999 Commands V Entry of V produces the confirmation display of correspondences between phenotypes and geno types First the number of map table to be viewed must be entered Enter number of locus to view gt I Here the ADA locus choice 1 has been selected which produces the following display ADA PHENO TYPE Genotype Phenotype Map AUCD Phenotype Genotype A A A AB A B AC A C B B B BG B C CLC Enter C to continue Entry of RETURN returns to the initial Edit Menu E Entry of E switches to Edit Mode first requiring entry of the number of the map table to be edit ed Enter number of locus to edit gt T When the map table has been selected the Edit Menu Display appears June 10 1999 GENOMAP e 21 7 Locus ADA PH E Mode of inheritance Phe
470. y relationships between phenotypes and genotypes of a loci that are not autosomal codominant or b autosomal codominant loci whose nomenclature does not conform to the PEDSYS conventions given in Appendix C Rules for Genotype and Phenotype Nomenclature Tables for one of more loci are kept in a Genotype Phenotype Map File generated by the program Introductory Display EDSYS program GENOMAP Copyright 1994 1999 SFBR GENOMAP is used to create and or edit a Genotype Phenotype Map File Enter C to CREATE a new Genotype Phenotype Map File E to EDIT a previously created Phenotype Genotype Map File Q to QUIT program 1 Creating a new Genotype Phenotype Map File Creation of a new Genotype Phenotype Map File choice C above results in the following display in which mode of inheritance is specified for generation of a Genotype Phenotype Map Table Autosomal codominant Al Autosomal dominant recessive A X linked codominant XI X linked dominant recessive XI Y linked YI Enter number corresponding to mode of inheritance gt 1 If autosomal codominant mode choice 1 is selected the following display appears Enter F to read Genotype Phenotype Map automatically from locus file K to enter Genotype Phenotype Map Table manually from keyboard Information for a Genotype Phenotype Map Table can be assembled from a file containing phenotyp ic or
471. y subset that do not meet criteria for inclusion in subset out in the same order as in the input file April 20 1999 SUBSET 43 3 subset cde defines the record structure of subset out nosubset cde defines the record structure of nosubset out Program limits IN and EX may be repeated up to 25 times each in a single run z 43 4 e SUBSET April 20 1999 TALLY Program TALLY generates cross tabulations and calculates distributions of items for any file for which an appropriate Code File has been constructed Introductory Display EDSYS program TALLY Copyright 1992 1999 SFBR TALLY generates cross tabulations and calculates distribution parameters for items in any file for which an appropriate Code File has been constructed 1 Unlinked File EXAI PLE LOCUS Sub directory number file name or O to quit When a file has been selected the following display appears The following operations can be performed on individual items either singly or in a two way tabulation for example NUMBER OF OFFSPRING by SEX 1 Frequency distribution 2 Distribution parameters mean variance skewness kurtosis 3 Both of the above Enter the number of the task to be performed gt 1 Frequency Distribution If the Frequency Distribution option has been selected choice 1 the following Item List Display appears EGO SEQUENTIAL ID 8 NUMBER OF OFFSPRING 15 Dam s
472. y the same record in duplic out Enter number above corresponding to your choice Q to quit program gt 1 This selection controls the output of unique and duplicate records Here we have chosen to generate an output file consisting of a subset of Example Master File records each of which will contain a unique Mate s Permanent ID All Mate s PIDs found in MASTER XMP will also be found in duplic out although in the latter file each will be found only once in this case on the record of Ego having the earliest birth date If choice 1 or 3 has been made the following display appears Single records will be saved in duplic out Save excluded records in noduplic out Y N gt If choice 2 has been made the following display is shown 18 2 DUPLIC April 20 1999 Duplicate records will be saved in duplic out Save excluded records in noduplic out Y N gt These options make it possible to divide the input file in various ways by saving records that do not fulfill the criteria for inclusion in duplic out Notes e DUPLIC requires that records be sorted in an order determined by the value of items selected and then comparing the record containing the first occurrence of any value with the value of entries in subsequent records e The compound sort in program DUPLIC provides some control over which record will be first in the list for comparison The major sort should be for the item or items select
473. ype tabulation without regard to offspring sex Segregation in Offspring of ALL ERS by FATHE 1 MATINGS INFERRED PHENOTYP UDED US PHENO TYPE ELES B C Offspring genotypes A A A B A C UNKNWN TOTAL 4 2 Offspring genotypes Father Mother A A A B A C UNKNWN TOTAL A B A B A B A B B B UNKNWN TOTAL Father Mother Offspring genotypes A A A B A C B B B B A B B B TOTAL May 21 1999 SEGCHECK e 37 7 Example 4 continued Offspring genotypes Father Mother A A A B A C B B C C UNKNWN TOTAL UNKNWN A B UNKNWN B B UNKNWN C C UNKNWN UNKNWN TOTAL Example 5 Table configuration choice 5 combined table of fathers with the same genotype tabulation by sex of offspring Segregation in Offspring of ALL ERS by MOTHE 1 MATINGS INFERRED PHENOTYP UDED US ADA PHENO TYPE ELES A B C Offspring genotypes Father A A A B A C B B B C C C UNKNWN TOTAL A A 37 8 SEGCHECK May 21 1999 Example 5 continued Offspring genotypes A A A B A C B B B C C C UNKNWN TOTAL Mother Father Offspring genotypes A A A B A C B B C C UNKNWN TOTAL UNKNWN
474. ype of parent i e SIRE or DAM as given in the UPDATE lt EXT gt file and lt parntid gt is the PID and lt sex gt is the sex i e M or F of the parent as it appears in the Master File These errors occur only when making changes to a record previously entered in the Master File Probable causes are a incorrect keyboard entry of parental PID b incorrect assignment of SEX to the 39 4 e SETMASTR April 20 1999 individual who is EGO s parent in the Master File or c incorrect assignment of SEX to the individual who is EGO s parent in UPDATE lt EXT gt To correct the errors If a re enter correct parental PID If b first change SEX of the individual in the Master File then re enter change of parental PID If c change SEX of the individual in the update file In any case use ALTMASTR in ALTER mode and re run SETMASTR using the most recent Update and Master files see note on renaming and deleting these files Important Warning The following messages Groups 5 7 result from errors in the Master File detected as the result of checking for the consistency of family structure before making the changes specified in UPDATE lt EXT gt These errors tend to be complex and may indicate serious problems with the data It is very important to examine closely the families in which these errors occur before assuming that changes have been made correctly As an example of what can go wrong consider the case in which assign

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