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TCGA-Assembler User Manual - Department of Health Studies

1. 34 ProcessmiRNASeqData lt function inputFilePath outputFileName outputFileFolder fileSource TCGA Assembler This function processes miRNASeq data file either acquired by TCGA Assembler module A or downloaded from Firehose website and imports the data into R It does the following 1 Save the miRNASeg read count data and reads per million miRNA mapped RPM data as two separate tab delimited txt files In each file the first column is the miRNA name The other columns are data of individual samples The first row in the file gives the TCGA sample barcodes refer to https wiki nci nih gov display TCGA TCGA barcode The file names are composed of outputFileName and either ReadCount txt or RPM txt with double underscore __ separating the two 2 Save the miRNASeq read count data and RPM data as two separate R data file rda each of which contains two variables The first variable is Des which is a single column character matrix including the miRNA names It serves as the description of the second variable Data which is a numeric matrix Each column in Data is a sample and each row corresponds to a miRNA The file names are composed of outputFileName and either ReadCount rda or RPM rda with double underscore __ separating the two parts For both read count and RPM the txt file and rda file contain the same data Having the same data in two different file formats is just for the convenience of using
2. 5 K N Save the gene level copy number data as an R data file rda which includes two variables The first variable is Des a character matrix including gene symbol chromosome ID and strand in the first second and third column respectively It describes the second variable Data which is a numeric matrix Each column in Data is a sample and each row corresponds to a gene The column names of Data are sample barcodes The file name is composed of outputFileName and rda The output txt file and rda file contain the same data Having the same data in two different file formats is for the convenience of using data under different software environments Input arguments inputFilePath a character string indicating the path of the input DNA copy number data file acquired by TCGA Assembler Module A or downloaded from Firehose outputFileName a character string to form the names of output files outputFileFolder a character string indicating the path of the directory to which the output files will be saved refGenomeFile a character string indicating the path of gene genomic position file that will be used There are two gene position files in the SupportingFiles folder of the package Use Hg18GenePosition txt or Hg19GenePosition txt if the input copy number data was generated based on reference genome Hg18 or Hg19 respectively Output argument A list object formed by two variables Des and Data Des is a character matrix of thr
3. UserManualExampleData RawData TCGA Assembler READ__broad mit edu__genome_wide_snp_6 _hg19__Jan 30 2014 txt outputFileName READ __genome_wide_snp_6 GeneLevelCNA outputFileFolder UserManualExampleData ProcessedData TCGA Assembler refGenomeFile SupportingFiles Hg19GenePosition txt Download and process humanmethylation450 data of six READ patient samples Methylation450RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation450 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG A01W 11 TCGA AG 3731 11 Methylation450Data ProcessMethylation450Data inputFilePath UserManualExampleData RawData TCGA Assembler READ__jhu usc edu__humanmethylation450__Jan 30 2014 txt outputFileName READ _humanmethylation450 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Calculate single value methylation data Methylation450_TSS1500_DHS CalculateSingleValueMethylationData input Methylation450Data regionOption TSS1500 DHSOption DHS outputFileName READ __humanmethylation450__SingleValue outputFileFolder UserManualExampleData ProcessedData TCGA Assembler chipAnnotationFile SupportingFiles MethylationChipAnnotation rda Download and
4. DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType BLCA assayPlatform genome_wide_snp_6 DownloadMethylationData lt function traverseResultFile saveFolderName cancerType assayPlatform inputPatientIDs NULL outputFileName This function downloads methylation data of specified cancer type measured by Illumina HumanMethylation27 BeadChip or Illumina HumanMethylation450 BeadChip It downloads the data files of individual samples and combines them into data matrix format The samples to be downloaded include tumors their matched normal tissues and control samples if exist Input arguments traverseResultFile a character string The path of the directory traverse result file that includes the URLs of all open access data files on TCGA server saveFolderName a character string The path of the directory to save the acquired data matrix files cancerType a character string indicating the cancer type for which to download data Options include ACC BLCA BRCA CESC COAD DLBC ESCA GBM HNSC KICH KIRC KIRP LAML LGG LIHC LUAD LUSC OV PAAD PRAD READ SARC SKCM STAD THCA UCEC UCS Look at https tcga data nci nih gov tcga for information about cancer types assayPlatform a character string indicating the assay platform used to generate the data Options include humanmethylation27 and humanmethylation450 inputPatientIDs a character
5. The second column is gene symbol The third column is chromosome id The fourth column includes genomic coordinates of CpG sites Starting from column five each column is the data of a sample and the first row gives the TCGA barcodes of samples Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions Acquire humanmethylation450 data of six rectum adenocarcinoma READ patient samples READ_Methylation450RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation450 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG AO1W 11 TCGA AG 3731 11 Acquire humanmethylation27 data of all rectum adenocarcinoma READ patient samples READ_Methylation27RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation27 DownloadmiRNASeqData lt function traverseResultFile saveFolderName cancerType assayPlatform miRNASeq inputPatientIDs NULL outputFileName This function downloads miRNASeq data of sp
6. sample The column names of Data are the TCGA barcodes of samples with their first 15 characters which indicate the tissue source site patient index and sample type Rows of Data are ordered so that genomic features of the same gene are adjacent in the matrix Des serves as the description of Data 22 Note If there are more than one sample of the same patient and the same tissue type measured by an assay platform which is actually a rare case only one of the samples will be kept for data combining Example In this example we will first download and process various kinds of data of several rectum adenocarcinoma READ patient samples and then merge them into single mega table using both the Intersect approach and Union approach The present working directory of R must be TCGA Assembler i e the package folder to run the examples rm list Is Clear workspace source Module_A r Load Module A functions source Module_B r Load Module B functions Download and process copy number data of six READ patient samples CNARawData DownloadCNAData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform genome_wide_snp_ 6 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AF 2692 10 TCGA AG 4021 10 GeneLevelCNA ProcessCNAData inputFilePath
7. All four data files have the same format Each row corresponds to a segment Column one is TCGA sample barcode Column two is chromosome id Column three is the start position of the segment Column four is the end position of the segment Column five is the number of probes in the segment 6 Column six is the copy number value transferred by base log copy number 2 centered on 0 For more details of the data format data type and data generation pipeline please refer to TCGA description at https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor read cgcc broad mit edu genome_wide snp_6 snp broad mit edu_LREAD Genome_Wide_SNP_6 mage tab 1 2003 0 DESCRIPTION txt Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples source Module_A r Load Module A functions Acquire copy number data of six rectum adenocarcinoma READ patient samples READ_CNARawData DownloadCNAData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform genome_wide_snp_ 6 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AF 2692 10 TCGA AG 4021 10 Acquire copy number data of all bladder urothelial carcinoma BLCA patient samples BLCA_CNARawData DownloadCNAData traverseResultFile
8. ProcessRPPADataWithGeneAnnotation 0 cece cece ence ence eee n tenets eee senescent tennant enaes 39 DownloadClinicalData lt function traverseResultFile saveFolderName cancerType clinicalDataType outputFileName This function downloads clinical data files of specified cancer type and save them in the specified folder Input arguments traverseResultFile a character string The path of the directory traverse result file that includes the URLs of all open access data files on TCGA server saveFolderName a character string The path of the directory to save downloaded clinical data files cancerType a character string indicating the cancer type for which to download data Options include ACC BLCA BRCA CESC COAD DLBC ESCA GBM HNSC KICH KIRC KIRP LAML LGG LIHC LUAD LUSC OV PAAD PRAD READ SARC SKCM STAD THCA UCEC UCS Look at https tcga data nci nih gov tcga for information about cancer types clinicalDataType a character vector indicating the types of clinical information to be obtained Options include patient drug follow_up and radiation patient indicates patient information including survival cancer grades and others drug indicates records of patient drug treatment follow_up indicates patient follow up information radiation indicates history of radiation therapy on patients outputFileName a character string used to form the names of downloaded data files It is the empty string
9. arguments A list object of character matrices containing the data and their descriptions retrieved from TCGA DCC Refer to the description of output data files for introduction of the contents in the character matrices Output data files This function can generate nine different types of data files each for one of the data types shown in the table above The name of an output data file includes six components 1 outputFileName 2 cancer type 3 institution that generated the data which can be unc edu or begsc ca 4 assay and post processing pipeline used to generate the data i e illuminaga_rnaseqv2 illuminaga_rnaseq illuminahiseq_rnaseqv2 or illuminahiseq_rnaseq 5 data type as shown in the table above 6 the date on which the input directory traverse result file was generated Double underscore __ is used to separate the six components in the file name If outputFileName is an empty string the file names consist of only the other five components For details of the formats of RNASeqV1 data types please refer to TCGA description at https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor read cgcc unc edu illuminaga_rnaseq rn aseq unc edu_READ IluminaGA_RNASeq mage tab 1 3 0 DESCRIPTION txt For details of the formats of RNASeqV2 data types please refer to TCGA description at https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor read cgcc unc edu illuminahiseq_rnaseq v2 rnaseqv2
10. count data and generate different types of data For details of RNASeqV1 and RNASeqV2 pipelines and the data files 37 generated by them please refer to https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor brca cgcc unc edu illuminahiseq_rnaseq v2 rnaseqv2 unc edu_BRCA IluminaHiSeq_RNASeqV2 mage tab 1 7 0 DESCRIPTION txt Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions source Module_B r Load Module B functions Download normalized gene expression data and exon expression data of six rectum adenocarcinoma READ patient samples which were generated by RNASeqV2 pipeline RNASeqRawData DownloadRNASeqData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform RNASeqV2 dataType c rsem genes normalized_results exon_quantification inputPatientIDs c TCGA EI 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG 3732 11 TCGA AG 3742 11 Process the downloaded normalized gene expression data and save the results to the ProcessedData TCGA Assembler subfolder GeneExpData ProcessRNASeqData inputFilePath UserManualExampleData RawData TCGA Assembler READ _unc edu_illuminahiseq_r
11. expression protein expression DNA Methylation DNA copy number and miRNA expression To match genomic features the data must contain the information of genes associated with the genomic features such as through the gene symbols in Des variable produced by many data processing functions in this package DNA copy number data must be preprocessed by the ProcessCNAData function to get gene level copy number values for combining with data from other platforms Input argument inputDataList a vector of list objects Each element in the vector is a list object of three variables that represent one dataset to be combined The names of the three variables are Des Data and dataType Des is a character matrix including descriptions of genomic features One column in Des must be gene symbols and with a column name of GeneSymbol because matching of genomic features is based on this column Data is a numeric matrix containing the data Each row is a genomic feature and each column is a sample The column names must be the TCGA sample barcodes refer to https wiki nci nih gov display TCGA TCGA barcode dataType is a character string indicating the type of data Options of dataType include GeneExp ProteinExp Methylation CNA and miRNAExp standing for gene expression protein expression DNA methylation DNA copy number and miRNA expression respectively combineStyle a character string indicating how the samples should be combined Intersect whic
12. running the examples rm list Is Clear workspace source Module_A r Load Module A functions source Module_B r Load Module B functions Download humanmethylation450 data of six rectum adenocarcinoma READ patient samples Methylation450RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation450 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG A01W 11 TCGA AG 3731 11 Process the downloaded humanmethylation450 data and save the results to ProcessedData TCGA Assembler subfolder Methylation450Data ProcessMethylation450Data inputFilePath UserManualExampleData RawData TCGA Assembler READ__jhu usc edu__humanmethylation450__Jan 30 2014 txt outputFileName READ _humanmethylation450 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Process READ HumanMethylation450 data downloaded from Firehose website Methylation450Data ProcessMethylation450Data inputFilePath UserManualExampleData RawData Firehose READ methylation _humanmethylation450__jhu_usc_edu __Level_3__within_bioassay_data_set_function__data data txt outputFileName READ _humanmethylation450 outputFileFolder UserManualExampleData ProcessedData Firehose fileSource Firehose
13. 2 pipeline The input data files should be either acquired by TCGA Assembler Module A or downloaded from Firehose website This function does the following 1 For gene expression data check whether the gene symbols are official HGNC gene symbols If not correct them 2 Extract most useful measurements from the input data files For RNASeqV1 gene expression data and exon expression data extract the RPKM values For RNASeqV2 normalized gene expression data extract the normalized count values For RNASeqV2 exon expression data extract the RPKM values 3 Draw and save a box plot of log2 transferred gene expression data for quality control purpose The picture file name is composed of outputFileName and __boxplot png 4 Save the extracted data as a tab delimited Gr file For gene expression data the first two columns are gene symbol and Entrez ID And the other columns are samples with TCGA sample barcodes in the top row refer to https wiki nci nih gov display TCGA TCGA barcode For exon expression data the first column is exon ID And the other columns are samples with TCGA sample barcodes in the top row 5 Save the extracted data as an R data file rda which includes two variables Des and Data Des is a character matrix including gene symbols and Entrez IDs for gene expression data and exon IDs for exon expression data Des describes the second variable Data which is a numeric matrix Each column in Data is a sample an
14. 5 NEE NEE NEEN ER walle ENER ENN ENEE EES EEN nas 6 DownloadMethylationData cece cece eee ee nee ne nee e eee EEE EEE Eee een cen ce cee bE EEE bE EERE EEE EES 8 DownloadmiRNASeoata cece cece neess een seese sesse rsrsrs EEE EEE EEE EEE EEE en seed e EEE EEE EEE EEE Es 10 D wnloadRNASegData ccc cece cee cee enn enn Een EEE REDE EEE EEE REED EEE EEE EEE EERE EEE EEE EEE EEE EE 12 DownloadRPPADatas ecco DEER get das EE ENEE EEN dE cea EE de T BEER Pains 14 TraverseAllDirectorieS nenoai e a see ee det Ste Ee ue eck 16 Module B includes the following functions CalculatesingleyaluehMerbvlattonfata ccc ccc cence nee een enn n eee ne EEE Eee eee e EEE EEE eee eb EEE EES 17 ChEcCkGEneSy MbOlssiairatecatevale tare datetate erer ed 20 CombineMultiPlatformData 0 0 cece ccc eee eee eee ne ene nen EE A E EEE Eee E EE et EEE aaaea 22 Extract lissueSpecificSampleSci 0 55 4s coated sde dav evens soa AEN AER eg de ee AS 25 MergeMetbvlationfata 00 ccc ccc cece enn eee eee e een EEE EEE EEE EE EEE EEE EEE EEE EEE EEE EEE ES 27 ProcessCNAD ate ineei aine Sex vies sien ay Shale aes Moe see wise th whoa de libel E R oan BY eee wee poe 29 ProcessMethylation2 TEE EE 31 ProcessMethylation450Data 0 0 ccc cece ence een RE AKEE INAN EE Eee EEE EEE EEE Een EEE EEE EEE AWER ADN 33 ProcessmIRNASEGData e333 cee AE AE tie Eege NA eher da bea wna Ehe ue af 35 ProcessSRNASeqDatancs ccvininuie aiiih iawn AREE EEE AE FEANEN NEE Midst Wea anos vawaw dane 37
15. C gene symbols If not correct them 3 When a protein is encoded by more than one gene duplicate the measurement of the protein a row in the data matrix for each gene 4 Draw and save a box plot picture of the data for quality control purpose The picture file name is composed of outputFileName and __ boxplot png 5 Save protein expression data as a tab delimited txt file The first column gives gene symbols The second column gives protein antibody names The other columns are data of individual samples The first row gives TCGA sample barcodes refer to https wiki nci nih gov display TCGA TCGA barcode 6 Save the processed data as an R data file rda which includes two variables Des and Data Des is a character matrix including two columns i e gene symbol and protein antibody name It serves as the description of the second variable Data which is a numeric matrix Each column in the data matrix is a sample and column names are TCGA sample barcodes The output txt file and rda file contain the same protein expression data Having the same data in two different file formats is just for the convenience of using the data under different software environments Input arguments inputFilePath a character string indicating the path of the input RPPA protein expression data file acquired by TCGA Assembler Module A or downloaded from Firehose website It should be a tab delimited txt file outputFileName a character st
16. Data TCGA Assembler READ__jhu usc edu__humanmethylation450__Jan 30 2014 txt outputFileName READ _humanmethylation450 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Merge the humanmethylation27 data and humanmethylation450 data Methylation27_450_ Merged MergeMethylationData input1 Methylation27Data input2 Methylation450Data outputFileName READ humanmethylation27_450_ merged outputFileFolder UserManualExampleData ProcessedData TCGA Assembler 28 This function processes DNA copy number data files acquired by TCGA Assembler Module A or downloaded from Firehose website and imports the data into R It does the following 1 Calculate gene level copy number value which is the average copy number of the genomic region of a gene 2 For gene level copy number data check and correct the gene identifiers to official gene symbols 3 Draw and save a box plot of the gene level copy number data for quality control purpose The picture file name is composed of outputFileName and boxplot png 4 Save the gene level copy number data as a tab delimited txt file The first three columns are descriptions of genomic features including gene symbol chromosome ID and strand The other columns are data of individual samples The first row gives TCGA sample barcode see reference at https wiki nci nih gov display TCGA TCGA barcode The file name is composed of outputFileName and txt
17. S 5 UTR 5 untranslated region 1stExon first exon Body gene body 3 UTR 3 untranslated region All all CpG sites associated with a gene no matter which genomic region the CpG sites are in For details about the definitions of the region options please refer to the Illumina annotations TSS1500 region includes TSS200 region as a subset 17 DHSOption a character string that can be DHS notDHS or Both indicating whether only CpG sites that are DNAse hypersensitive will be included in the calculation DHS selects CpG sites that are DNAse hypersensitive notDHS selects CpG sites that are not labeled as DNAse hypersensitive Both selects all CpG sites no matter whether they are DNAse hypersensitive or not The DNAse hypersensitivity of CpG sites are experimentally determined and provided by Illumina chip annotations outputFileName a character string used to form the names of output data files and box plot picture file outputFileFolder a character string indicating the directory in which the output files will be saved chipAnnotationFile a character string indicating the path of the chip annotation file to be used by the function which is the MethylationChipAnnotation rda file in the SupportingFiles folder in the package Output argument A list object of two variables The first variable is Des a two column character matrix including gene symbol and the single value type that shows the regionOption and DHSOption used to calculat
18. TCGA Assembler User Manual Yitan Zhu Yuan Ji 1 Center for Biomedical Research Informatics NorthShore University HealthSystem Evanston IL 60201 2 Department of Health Studies The University of Chicago Chicago IL 60637 Email zhuyitan gmail com Feb 4 2014 CAUTION We identified a defect in Mac application Preview app Do not open this pdf file in Preview and copy paste the R code for testing Instead use Adobe Reader hitp get adobe con reader or Acrobat to open this pdf file and copy paste code to R for testing Introduction TCGA Assembler can acquire and process most of TCGA public data including level 3 data of RNA seq DNA methylation DNA copy number protein expression and miRNA seq and also de identified patient clinical information To download TCGA Assembler go to http health bsd uchicago edu yji TCGA Assembler htm Click on Download Software and unzip the downloaded files to your desired location The folder of the package is TCGA Assembler The TCGA Assembler package includes two modules Module A and Module B The following gives a brief introduction of the contents in the package Module_A r includes all Module A functions Module A downloads data from the open access HTTP directory of TCGA Data Coordinating Center DCC the Uniform Resource Locator URL of which is https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor Each sample in TCGA has one or multipl
19. _RPPA_Core Level_3 1 0 0 DESCRIPTION txt Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples 14 source Module_A r Load Module A functions Acquire RPPA protein expression data of six rectum adenocarcinoma READ patient samples READ_RPPARawData DownloadRPPAData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform mda_rppa_core inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG 3582 01 TCGA AG 4001 01 Acquire RPPA protein expression data of all bladder urothelial carcinoma BLCA patient samples BLCA_RPPARawData DownloadRPPAData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType BLCA assayPlatform mda_rppa_core 15 This function traverses sub directories in the open access HTTP directory on TCGA DCC data server and obtains the URLs of public TCGA data files The URLs will be saved in a rda file in the present working directory The file name is composed of the input argument fileLabel and the date on which this function is executed Thus through the file name we can tell how old the URL information included in the file is Input arguments entryPoint URL of th
20. a_rppa_core inputPatientIDs c TCGA EI 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG 3582 01 TCGA AG 4001 01 Process the downloaded protein expression data and save the results in UserManualExampleData ProcessedData TCGA Assembler RPPAData ProcessRPPADataWithGeneAnnotation inputFilePath UserManualExampleData RawData TCGA Assembler READ__mdanderson org _mda_rppa_core__Jan 30 2014 txt outputFileName READ _mda_rppa_core outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Process RPPA protein expression data file downloaded from Firehose website RPPAData ProcessRPPADataWithGeneAnnotation inputFilePath UserManualExampleData RawData Firehose READ RPPA_AnnotateWithGene txt outputFileName READ _mda_rppa_core outputFileFolder UserManualExampleData ProcessedData Firehose 40
21. ad Module B functions Download humanmethylation27 data of six rectum adenocarcinoma READ patient samples Methylation27RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation27 inputPatientIDs c TCGA AG 3583 01 TCGA AG A032 01 TCGA AF 2692 11 TCGA AG 4001 01 TCGA AG 3608 01 TCGA AG 3574 01 Process the downloaded humanmethylation27 data and import the data into R Methylation27Data ProcessMethylation27Data inputFilePath UserManualExampleData RawData TCGA Assembler READ__jhu usc edu__humanmethylation27__Jan 30 2014 txt outputFileName READ _humanmethylation27 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Download humanmethylation450 data of six READ patient samples Methylation450RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation450 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG A01W 11 TCGA AG 3731 11 Process the downloaded humanmethylation450 data and import the data into R Methylation450Data ProcessMethylation450Data inputFilePath UserManualExampleData Raw
22. an 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform miRNASeq inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AF 2689 11 TCGA AF 2691 11 Process the downloaded READ miRNA seq data and save the results to the ProcessedData TCGA Assembler subfolder miRNASeqData ProcessmiRNASeqData inputFilePath UserManualExampleData RawData TCGA Assembler READ__bcgsc ca__illuminahiseq_mirnaseq__NCBI36__Jan 30 2014 txt outputFileName READ illuminahiseq_mirnaseq outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Process READ miRNA seq data downloaded from Firehose website and save the results to the ProcessedData Firehose subfolder miRNASeqData ProcessmiRNASeqData inputFilePath UserManualExampleData RawData Firehose READ mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_ 3__miR_gene_expression__data data txt outputFileName READ _ illuminaga_mirnaseq outputFileFolder UserManualExampleData ProcessedData Firehose fileSource Firehose 36 This function processes RNASeq data files and imports data into R including 1 gene expression data file generated by RNASeqV1 pipeline 2 exon expression data file generated by RNASeqV1 pipeline 3 normalized gene expression data file generated by RNASeqV2 pipeline and 4 exon expression data file generated by RNASeqV
23. by default Output clinical data files Please refer to TCGA http cancergenome nih gov for information about the clinical data format The downloaded clinical data files have names composed of outputFileName and their original file names with __ separating the two If outputFileName is an empty string the names of the downloaded data files are the same as their original file names on TCGA DCC Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples source Module_A r Load Module A functions Acquire clinical information of bladder urothelial carcinoma BLCA and rectum adenocarcinoma READ patients DownloadClinicalData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType BLCA clinicalDataType c patient drug follow_up radiation DownloadClinicalData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ clinicalDataType c patient drug DownloadCNAData lt function traverseResultFile saveFolderName cancerType assayPlatform genome_wide_snp_6 inputPatientIDs NULL outputFileName 7 This function downloads copy number data of samples belonging to the specified cancer type and measured by the specified assay platform The sam
24. d each row corresponds to a gene or exon The column names of Data are TCGA sample barcodes Input arguments inputFilePath a character string indicating the path of input RNASeq data file acquired by TCGA Assembler Module A or downloaded from Firehose website It should be a tab delimited txt file outputFileName a character string to form the names of output files outputFileFolder a character string indicating the directory in which the output files will be saved dataType a character string indicating the type of input data file GeneExp indicates that the input file is gene expression data ExonExp indicates that the input file is exon expression data verType a character string indicating the data processing pipeline used to generate the data Options include RNASeqV1 and RNASeqvV2 Output argument A list object of two variables Des and Data If dataType is GeneExp Des is a character matrix of two columns including gene symbols and Entrez IDs It describes the second variable Data which is a numeric matrix of gene expressions Each column in the matrix is a sample and each row corresponds to a gene The column names of Data are TCGA sample barcodes If dataType is ExonExp Des is a single column character matrix of exon IDs Data is a numeric matrix of exon expressions Each column in the data matrix is a sample and each row corresponds to an exon Note RNASeqV1 and RNASeqV2 are two different pipelines used to process RNA seq read
25. e data files produced by each assay platform Module A assembles the data files of individual samples into data matrices where each row is a genomic feature and each column is a sample Module_B r includes all Module B functions Module B processes data matrix files to fulfill various data manipulation needs Module B can process both data matrix files assembled by TCGA Assembler Module A and data matrix files downloaded from Firehose website at the Broad Institute https confluence broadinstitute org display GDAC Dashboard Stddata QuickStartGuide_Examples r includes the code of all examples in TCGA Assembler Quick Start Guide DirectoryTraverseResult_Jan 30 2014 rda is an R data file including the URLs of all TCGA open access data files It was generated by running the TraverseAllDirectories function in Module A on Jan 30 2014 SupportingFiles folder includes supporting files and annotation files used by Module B functions UserManualExampleData folder holds some data files either acquired processed by TCGA Assembler or downloaded from Firehose website which will be used by the examples in this user manual There are four subfolders in the UserManualExampleData folder The RawData TCGA Assembler subfolder is used to hold data downloaded from TCGA DCC by TCGA Assembler The ProcessedData TCGA Assembler subfolder is used to contain results obtained by processing the raw data files in the RawData TCGA Assembler subfolder The RawData Firehos
26. e directory on TCGA DCC server that needs to be traversed To obtain the URLs of all open access TCGA data files use https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor as the entry point fileLabel a string to be included in the name of the file to store the traverse results Output directory traverse result file The name of the directory traverse result file is composed of the input argument fileLabel and the date on which this function is executed There are three variables included in the file file_url a character vector including the URLs of all data files under the entryPoint upper_file_url the same as file_url except that all characters in upper_file_url are in uppercase to facilitate case insensitive string matching dir_url a character vector including the URLs of all sub directories under the entryPoint Note Currently there are about 1 300 000 data files and 18 000 sub directories based on numbers obtained in Jan 2013 in the open access directory on TCGA DCC data server To traverse all the sub directories takes about an hour to complete depending upon Internet connection speed A good thing is that it needs to be done only once for downloading the data of all various cancer types and assay platforms In the package we include a directory traverse result file obtained on Jan 30 2014 The file name is DirectoryTraverseResult_Jan 30 2014 rda which includes the URLs of all public data fi
27. e multi platform data using Intersect approach MergedData CombineMultiPlatformData inputDataList inputDataList Merge multi platform data using Union approach MergedData CombineMultiPlatformData inputDataList inputDataList combineStyle Union 24 ExtractTissueSpecificSamples lt function inputData tissueType singleSampleFlag sampleTypeFile SupportingFiles TCGASampleType txt This function extracts from the input data matrix a subset of the data belonging to the specified tissue types Input arguments inputData a numeric matrix containing data Each row is a genomic feature and each column is a sample The column names of the data matrix must be TCGA sample barcodes which must start with TCGA and have a length no shorter than 15 characters Refer to https wiki nci nih gov display TCGA TCGA barcode for details of TCGA barcodes tissueType a character vector indicating for which tissue types to extract data The first column in the following table gives the options of tissueType The second column gives the interpretation of the options And the third column shows the sample categories i e tumor or normal Option Tissue Type Category TP Primary Solid Tumor Tumor TR Recurrent Solid Tumor Tumor TB Primary Blood Derived Cancer Peripheral Blood Tumor TRBM Recurrent Blood Derived Cancer Bone Marrow Tumor TAP Additional New Primary Tumor TM Metas
28. e subfolder contains data files downloaded from the Firehose website We keep only several samples in the Firehose data files to make their sizes small so that they can be included in the package and the data formats are not changed The ProcessedData Firehose subfolder is used to contain results obtained by processing the Firehose data files in the RawData Firehose subfolder Because downloading and processing TCGA data may require significant memory space depending on the size of data we recommend using TCGA Assembler on computers with 16GB or larger RAM To use TCGA Assembler R and R packages including HGNChelper RCurl httr stringr digest bitops and their dependent packages need to be installed They are freely available from http www r project org General Procedure of Using TCGA Assembler Pipeline Step 1 Step 2 Step 3 Step 4 Step 5 Start R and set the TCGA Assembler folder i e the package folder as the Present Working Directory PWD of R Execute Module A function TraverseAllDirectories to traverse all open access directories on TCGA DCC data server to gather the URLs of all public data files Due to the vast amount of sub directories 18 000 and files 1 300 000 this traverse process can take about an hour to complete depending upon the Internet connection speed A good thing is that it needs to be done only once to download TCGA public data of all cancer types and assay platforms Use the data f
29. e symbol 4 Draw and save a box plot of the data for quality control purpose The picture file name is composed of outputFileName and __boxplot png 5 Save the processed data as a tab delimited Get file The first four columns are Illumina ID of CpG site gene symbol chromosome ID and genome coordinate The other columns are data of individual samples The top row gives the TCGA sample barcodes refer to https wiki nci nih gov display TCGA TCGA barcode 6 Save the processed data as an R data file rda which includes two variables Des and Data Des is a character matrix including the four column description of CpG sites It serves as the description of Data which is a numeric matrix Each column in the data matrix is a sample and the column names are sample barcodes The output txt file and rda file contain the same data Having the same data in two different file formats is for the convenience of using data under different software environments Input arguments inputFilePath a character string indicating the path of input data file acquired by TCGA Assembler Module A or downloaded from Firehose website It should be a tab delimited txt file outputFileName a character string to form the names of output files outputFileFolder a character string indicating the path of the directory to which the output files will be saved fileSource a character string either TCGA Assembler or Firehose TCGA Assembler which is the de
30. e the data with in between to separate them Des serves as the description of the second variable Data which is a numeric data matrix Each column in the data matrix is a sample and each row corresponds to a gene The column names of Data are the TCGA barcodes of samples Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions source Module_B r Load Module B functions Download humanmethylation450 data of six rectum adenocarcinoma READ patient samples Methylation450RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation450 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG A01W 11 TCGA AG 3731 11 Process the downloaded humanmethylation450 data and import the data into R Methylation450Data ProcessMethylation450Data inputFilePath UserManualExampleData RawData TCGA Assembler READ__jhu usc edu__humanmethylation450__Jan 30 2014 txt outputFileName READ _humanmethylation450 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Calculate average methylation values of all CpG sites associated with the genes Met
31. ecified cancer type It downloads the data files of individual samples and combines them into data matrices The samples to be acquired include tumors their matched normal tissues and control samples if exist Input arguments traverseResultFile a character string The path of the directory traverse result file that includes the URLs of all open access data files on TCGA server saveFolderName a character string The path of the directory to save the acquired data matrix files cancerType a character string indicating the cancer type for which to download data Options include ACC BLCA BRCA CESC COAD DLBC ESCA GBM HNSC KICH KIRC KIRP LAML LGG LIHC LUAD LUSC OV PAAD PRAD READ SARC SKCM STAD THCA UCEC UCS Look at https tcga data nci nih gov tcga for information about cancer types assayPlatform a character string indicating the assay platform used to generate the data Currently the only option allowed is miRNASeq It acquires data generated by both illuminaga_mirnaseq assay and illuminahiseq_mirnaseq assay if the data exist inputPatientIDs a character vector that includes TCGA barcodes of the patients samples the data of which should be obtained If it is NULL by default data of all samples in the specified cancer category will be acquired Barcodes in inputPatientIDs must start with TCGA but do not need to be full length and complete because string matching for identifying the samples data starts
32. ee columns including gene symbol chromosome ID and strand in the first second and third column respectively It describes the second variable Data which is a numeric matrix of gene level copy number Each column in Data is a sample and each row corresponds to a gene The column names of Data are sample barcodes Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions 29 source Module_B r Load Module B functions Download DNA copy number data of six rectum adenocarcinoma READ patient samples CNARawData DownloadCNAData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform genome_wide_snp_6 inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AF 2692 10 TCGA AG 4021 10 Process the downloaded copy number data and calculate an average copy number for each gene Save results to subfolder ProcessedData TCGA Assembler in the UserManualExampleData folder READ GeneLevel CNA ProcessCNAData inputFilePath UserManualExampleData RawData TCGA Assembler READ__broad mit edu__genome_wide_snp_6 hg19__Jan 30 2014 txt outputFileName READ__genome_wide_snp_6 GeneLevelCNA outputFileFolder UserManua
33. essMethylation27Data inputFilePath UserManualExampleData RawData TCGA Assembler READ__jhu usc edu__humanmethylation27__Jan 30 2014 txt outputFileName READ _humanmethylation27 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Des Methylation27DataSDes We purposely make an symbol error to simulate mistakes that Excel may make by transferring gene symbol to date format ID which Des GeneSymbol SEPT7 SEPT7 is an official gene symbol Change SEPT7 to a wrong gene symbol in date format Des ID GeneSymbol 7 Sep Check and Correct gene symbol using the CheckGeneSymbol function 20 Des CheckGeneSymbol Des print Des ID GeneSymbol 21 This function combines multi platform datasets into a single mega data table through matching of patient samples and genomic features There are two possible ways to match patient samples across platforms One is to identify samples measured by all assay platforms and merge the multi platform data of these common samples which is called Intersect and also the default setting of this function The other is to include a sample as long as it is measured by at least one assay platform which is called Union Matching genomic features refers to putting together the multi platform data of the same gene i e making them adjacent rows in the data table Currently this function works on combining five different types of data including gene
34. essMethylation450Data or MergeMethylationData function Another way to generate this list object is to load the rda data file produced by the ProcessMethylation27Data or ProcessMethylation450Data function and form a list using the loaded Des and Data input2 a list object containing the other methylation dataset to be merged which should be generated in the same way as input1 outputFileName a character string to form the names of output files outputFileFolder a character string indicating the path of the directory in which the output files will be saved Output argument A list object formed by two variables The first variable is Des which is a character matrix including a four column description of CpG sites i e Illumina ID of CpG site gene symbol chromosome ID and genomic coordinate It serves as the description of the second variable Data which is a numeric matrix Each column in Data corresponds to a sample and the column names of Data are TCGA barcodes of samples Note MergeMethylationData function can be used to merge only methylation datasets that include Illumina IDs of CpG sites as description It can NOT be used to merge methylation dataset without Illumina IDs of CpG sites 27 Example The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions source Module_B r Lo
35. f data should be acquired The following table shows the available options when assayPlatform is RNASeqV1 or RNASeqV2 Multiple types of data can be acquired simultaneously assayPlatform RNASeqvV1 assayPlatform RNASeqv2 Gene expression values Gene expression values estimated by RSEM algorithm Exon expression rsem genes normalized_r Normalized gene expression gene quantification rsem genes results exon quantification values esults values a BE Splice junction Isoform expression values spljxn quantification rsem isoforms results expression values estimated by RSEM algorithm rsem isoforms normalize Normalized isoform expression d_results values exon_quantification Exon expression values Splice junction expression junction_quantification values inputPatientIDs a character vector that includes TCGA barcodes of the patients samples whose data should be obtained If it is NULL by default data of all samples in the specified cancer category will be acquired Barcodes in inputPatientIDs must start with TCGA but do not need to be full length and complete because string matching for identifying the samples data starts from the beginning of the barcodes For details of TCGA barcodes refer to https wiki nci nih gov display TCGA TCGA barcode 12 outputFileName a character string used to form the names of obtained data files It is the empty string by default Output
36. fault setting indicates that the input data file was acquired by TCGA Assembler Module A and Firehose indicates that the input data file was downloaded from Firehose website Output argument A list object of two variables which are Des and Data Des is a character matrix of the four column description of CpG sites including Illumina ID of CpG site gene symbol chromosome ID and genomic coordinate It serves as the description of the second variable Data which is a numeric matrix Each column in the matrix is a sample and the column names are the TCGA sample barcodes Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace 31 source Module_A r Load Module A functions source Module_B r Load Module B functions Download humanmethylation27 data of six rectum adenocarcinoma READ patient samples Methylation27RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation27 inputPatientIDs c TCGA AG 3583 01 TCGA AG A032 01 TCGA AF 2692 11 TCGA AG 4001 01 TCGA AG 3608 01 TCGA AG 3574 01 Process the downloaded humanmethylation27 data and save the results to UserManualExampleData ProcessedData TCGA Assembler Methylation27Data ProcessMe
37. fer to https wiki nci nih gov display TCGA TCGA barcode outputFileName a character string used to form the names of obtained data files It is the empty string by default Output arguments A character matrix containing the data and their descriptions retrieved from TCGA DCC Refer to the description of output data file for introduction of the content in the character matrix Output data file The name of the output data file includes five components 1 outputFileName 2 cancer type 3 institution that generated the data which is mdanderson org 4 assay platform used to generate the data i e mda_rppa_core 5 the date on which the input directory traverse result file was generated Double underscore __ is used to separate the five components in the file name If outputFileName is an empty string the file names consist of only the other four components The output data file is a tab delimited txt file containing RPPA protein expression data in matrix format The top row gives the TCGA barcodes of samples The first column shows protein antibody name after and corresponding gene symbols before that encode the protein Starting from the second column each column corresponds to a sample For details about how the data were generated and normalized please refer to https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor read cgcc mdanderson org mda_rppa_c ore protein_exp mdanderson org READ MDA
38. from the beginning of the barcodes For details of TCGA barcodes refer to https wiki nci nih gov display TCGA TCGA barcode outputFileName a character string used to form the names of obtained data files It is the empty string by default Output arguments A list object of character matrices containing the data and their descriptions retrieved from TCGA DCC Refer to the description of output data files for introduction of the contents in the character matrices Output data files For both illuminaga_mirnaseq assay and illuminahiseq_mirnaseq assay there will be two output data files The name of an output data file includes six components 1 outputFileName 2 cancer type 3 institution that generated the data i e bcgsc ca 4 assay used to generate the data i e illuminaga_mirnaseq or illuminahiseq_mirnaseq 5 reference genome used i e NCBI36 or GRCh37 6 the date on which the input directory traverse result file was generated Double underscore __ is used to separate the six components in the file name If outputFileName is an empty string the file names consist of only the other five components The two output data files of the same platform differ in the reference genome used to map the reads NCBI36 and GRCh37 indicate Hg18 and Hg19 reference genomes respectively Both files are tab delimited txt files containing the miRNA expression data in matrix format In the files the first row gives TCGA barcodes of samples and
39. h is the default setting selects samples that are measured by all assay platforms Union includes a sample as long as it is measured by at least one assay platform Output argument A list object of two variables Des and Data Des is a character matrix including descriptions of genomic features Des has three columns The first column is gene symbol The second column is platform which can be GE PE ME CN and miRExp representing gene expression protein expression methylation copy number and miRNA expression respectively The third column is a description of genomic features If the platform is GE the description is Entrez ID of the gene If the platform is PE the description is the name of the protein antibody used in the RPPA assay For CN platform the description shows the chromosome ID and strand of gene For miRExp platform the description column is empty For ME platform if the data are single value methylation data calculated by the CalculateSingleValueMethylationData function the description column gives the single value type indicating how the data were calculated refer to CalculateSingleValueMethylationData function for the definition of single value type if the data are methylation data of CpG sites the description column gives the Illumina ID chromosome ID and genomic coordinate of the CpG sites with separating them Data is a numeric matrix including the merged data Each row is a genomic feature and each column is a
40. her acquired by TCGA Assembler Module A or downloaded from Firehose website It should be a tab delimited txt file outputFileName a character string to form the names of output files outputFileFolder a character string indicating the directory in which the output files will be saved fileSource a character string either TCGA Assembler or Firehose TCGA Assembler which is the default setting indicates that the input data file was acquired by TCGA Assembler Module A and Firehose indicates that the input data file was downloaded from Firehose website Output argument A list object formed by Des and Data Des is a character matrix of four column descriptions of CpG sites including Illumina ID of CpG site gene symbol chromosome ID and genomic coordinate It serves as the description of the second variable Data which is a numeric matrix Each column in Data is a sample and the column names of Data are TCGA sample barcodes Note For HumanMethylation450 data file downloaded from Firehose this function calls GetMethylation450Data function to read in the data file and get rid of the redundant columns of CpG site descriptions 33 GetMethylation450Data function reads and processes the data file block by block to circumvent potential memory limitation problem caused by large sizes of Firehose data files gt 10GB for some cancer types Examples The present working directory of R must be TCGA Assembler i e the package folder for
41. hylation450_All_ Both CalculateSingleValueMethylationData input Methylation450Data regionOption All DHSOption Both outputFileName READ __humanmethylation450__SingleValue outputFileFolder UserManualExampleData ProcessedData TCGA Assembler chipAnnotationFile SupportingFiles MethylationChipAnnotation rda Calculate average methylation values of CpG sites within TSS200 region of the genes Methylation450_TSS200_ Both CalculateSingleValueMethylationData input Methylation450Data regionOption TSS200 DHSOption Both outputFileName 18 READ __humanmethylation450___SingleValue outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Calculate average methylation values of CpG sites that are within TSS1500 region of the genes and are DNAse hypersensitive Methylation450_TSS1500_DHS CalculateSingleValueMethylationData input Methylation450Data regionOption TSS1500 DHSOption DHS outputFileName READ __humanmethylation450__SingleValue outputFileFolder UserManualExampleData ProcessedData TCGA Assembler chipAnnotationFile SupportingFiles MethylationChipAnnotation rda 19 This function identifies obsolete gene symbols and gene symbol errors caused by auto conversion in spreadsheet programs like Excel and corrects them to official HGNC gene symbols Symbols that are not known errors obsolete gene symbols or official gene symbols will be
42. ich produces difficulties when loading the data into software environment for data analysis such as R 2 Check whether the gene symbols are official HGNC gene symbols If not correct them 3 When a CpG site corresponds to more than one gene symbol duplicate the measurements of the CpG site a row in the data matrix for each gene symbol that it stands for 4 Draw and save a box plot of the data for quality control purpose The picture file name is composed of outputFileName and __boxplot png 5 Save the processed data as a tab delimited Get file The first four columns are Illumina ID of CpG site gene symbol chromosome ID and genomic coordinate The other columns are data of individual samples And the top row shows the TCGA barcodes of samples refer to https wiki nci nih gov display TCGA TCGA barcode 6 Save the processed data as an R data file rda which contains two variables Des and Data Des is a character matrix including the four column description of CpG sites It serves as the description of the second variable Data which is a numeric matrix Each column in Data is a sample and the column names of Data are TCGA sample barcodes The output txt file and rda file contain the same data Having the same data in two different file formats is for the convenience of using data under different software environments Input arguments inputFilePath a character string indicating the path of the input data file eit
43. ile URLs obtained in Step 2 and other Module A functions whose names start with Download to 1 acquire TCGA public data of a specific cancer type and assay platform and 2 assemble the data files of individual samples into data matrices in tab delimited txt files Data matrix txt files generated by TCGA Assembler Module A or downloaded from Firehose website should be processed by corresponding Module B functions whose names start with Process These functions extract useful measurements from the txt files and import the data into R Data quality check removal of redundant information and some data calculation such as calculating gene level copy number values are fulfilled by these functions Based on the processed data generated in Step 4 use other data processing functions in Module B to do various data manipulations such as merging multi platform data into a single mega data table We included a directory traverse result file named DirectoryTraverseResult_Jan 30 2014 rda in the package It was generated by running the TraverseAllDirectories function on Jan 30 2014 The URLs of TCGA public data files are usually stable and valid for a quite long time So with this file you can skip Step 2 and directly run the examples of Module A functions in this user manual Contents Module A includes the following functions Download Clinical Data desse ES tues sassa sna tues sas amone a A a dah eeueeycetcemiewe 5 DownloadCNAData 0
44. into data matrix format The samples to be acquired include tumors their matched normal tissues and control samples if exist Input arguments traverseResultFile a character string indicating the path of the directory traverse result file that includes the URLs of all open access data files on TCGA server saveFolderName a character string The path of the directory to save the acquired data matrix files cancerType a character string indicating the cancer type for which to download data Options include ACC BLCA BRCA CESC COAD DLBC ESCA GBM HNSC KICH KIRC KIRP LAML LGG LIHC LUAD LUSC OV PAAD PRAD READ SARC SKCM STAD THCA UCEC UCS Look at https tcga data nci nih gov tcga for information about cancer types assayPlatform a character string indicating the assay platform and data pipeline used to generate the data Options include RNASeqV1 and RNASeqV2 The main difference between these two is the data post processing pipeline used RNASeqV1 generates three files for each sample including gene expression exon expression and junction expression RNASeqV2 generates six files for each sample including expression estimates of genes and isoforms normalized expression values of genes and isoforms expressions of exons and junctions Also this function acquires data generated by both illuminaga_mirnaseq assay and illuminahiseq_mirnaseq assay if the data exist dataType a character vector indicating which types o
45. lExampleData ProcessedData TCGA Assembler refGenomeFile SupportingFiles Hg19GenePosition txt Process READ copy number data downloaded from Firehose website and calculate average copy number value Save results to UserManualExampleData ProcessedData Firehose READ GeneLevel CNA ProcessCNAData inputFilePath UserManualExampleData RawData Firehose READ snp__genome_wide_snp_ 6 _broad_mit_edu__hg18 __Level_3__segmented_scna_hg18__ seg seg txt outputFileName READ __genome_wide_snp_6 GeneLevelCNA outputFileFolder UserManualExampleData ProcessedData Firehose refGenomeFile SupportingFiles Hg18GenePosition txt 30 ProcessMethylation27 Data lt function inputFilePath outputFileName outputFileFolder fileSource TCGA Assembler This function processes HumanMethylation27 BeadChip data file either acquired by TCGA Assembler Module A or downloaded from Firehose and imports the data into R It does the following 1 For data files downloaded from Firehose remove redundant columns in the data Firehose HumanMethylation27 data file includes replicated columns of probe descriptions i e gene symbol chromosome ID genomic coordinate which are identical for each sample 2 Check whether the gene symbols are official HGNC gene symbols If not correct them 3 When a CpG site corresponds to more than one gene symbol duplicate the measurements of the CpG site a row in the data matrix for each gen
46. left unchanged Input argument Des a character matrix containing the description of genomic features One column of the matrix MUST be gene symbol and its column name MUST be GeneSymbol Output argument The output is a character matrix with the same structure of Des but with the gene symbols checked and corrected Note If a symbol can not be uniquely mapped to one official gene symbol for example a symbol is the alias for more than one genes all official gene symbols that are associated with this alias will be included in the corrected gene symbol with triple underscore ___ separating each involved official gene symbol Example The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions source Module_B r Load Module B functions Download humanmethylation27 data of six rectum adenocarcinoma READ patient samples Methylation27RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylation27 inputPatientIDs c TCGA AG 3583 01 TCGA AG A032 01 TCGA AF 2692 11 TCGA AG 4001 01 TCGA AG 3608 01 TCGA AG 3574 01 Process the downloaded humanmethylation27 data and import the data into R Methylation27Data Proc
47. les existing on TCGA data server on Jan 30 2014 You can use this directory traverse result file to quickly start downloading TCGA data and skip the step of running the TraverseAllDirectories function The file URLs are usually stable and valid for quite a long time Example The present working directory of R must be TCGA Assembler i e the package folder for running the examples source Module_A r Load Module A functions Get the URLs of public data files of all cancer types and all assay platforms TraverseAllDirectories entryPoint https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor fileLabel DirectoryTraverseResult Get the URLs of all rectum adenocarcinoma READ public data files The output directory traverse result file can be used to download READ data generated by all different assay platforms TraverseAllDirectories entryPoint https tcga data nci nih gov tcgafiles ftp_auth distro_ftpusers anonymous tumor read fileLabel READ_DirectoryTraverseResult 16 CalculateSingleValueMethylationData lt function input regionOption DHSOption outputFileName outputFileFolder chipAnnotationFile SupportingFiles MethylationChipAnnotation rda This function does the following 1 Calculate an average methylation value for each gene based on certain CpG sites according to the specified option see details of regionOption and DHSOption 2 Draw and save a bo
48. me data in two different file formats is for the convenience of using data under different software environments Input arguments input a list object containing the methylation data based on which a single methylation value needs to be calculated for each gene This list object can be generated by the ProcessMethylation27Data ProcessMethylation450Data and MergeMethylationData functions It is a list object formed by two variables Des and Data Des is a four column character matrix including Illumina ID of CpG site gene symbol chromosome ID and genomic coordinate Data is a numeric matrix containing methylation data of samples where each column corresponds to a sample and the column names are the TCGA barcodes of samples Des serves as the description of Data Another way to generate this list object is to load the rda file produced by the ProcessMethylation27Data ProcessMethylation450Data and MergeMethylationData functions and form a list object using the loaded Des and Data variables regionOption a character string indicating for which genomic region of a gene the average methylation value should be calculated based on HumanMethylation450 BeadChip annotations provided by Illumina http support illumina com downloads humanmethylation450_15017482_v1 2_product_files ilmn Available options are TSS1500 TSS200 5 UTR 1stExon Body 3 UTR and All TSS1500 within 1500 bps of a Transcription Start Site TSS TSS200 within 200 bps of a TS
49. naseqv2__rsem genes normalized_results__Jan 30 2014 txt outputFileName READ illuminahiseq_rnaseqv2__GeneExp outputFileFolder UserManualExampleData ProcessedData TCGA Assembler dataType GeneExp verType RNASeqv2 Process the downloaded exon expression data and save the results to the ProcessedData TCGA Assembler subfolder ExonExpData ProcessRNASeqData inputFilePath UserManualExampleData RawData TCGA Assembler READ__unc edu__illuminahiseq_rnaseqv2__exon_quantification__Jan 30 2014 txt outputFileName READ illuminahiseq_rnaseqv2__ExonExp outputFileFolder UserManualExampleData ProcessedData TCGA Assembler dataType ExonExp verType RNASeqv2 Process RNASeqV1 gene expression data of READ samples which were downloaded from Firehose website GeneExpData ProcessRNASeqData inputFilePath UserManualExampleData RawData Firehose READ rnaseq___illuminaga_rnaseq__unc_edu__Level_3__ge ne_expression__data data txt outputFileName READ _ illuminaga_rnaseq__GeneExp outputFileFolder UserManualExampleData ProcessedData Firehose dataType GeneExp verType RNASeqV1 38 This function processes RPPA data files either acquired by TCGA Assembler Module A or downloaded from Firehose website and imports the data into R It does the following 1 Split the gene symbol and protein antibody name into two separate columns 2 Check whether the gene symbols are official HGN
50. on27 inputPatientIDs c TCGA AG 3583 01 TCGA AG A032 01 TCGA AF 2692 11 TCGA AG 4001 01 TCGA AG 3608 01 TCGA AG 3574 01 Process the downloaded humanmethylation27 data and import the data into R Methylation27Data ProcessMethylation27Data inputFilePath UserManualExampleData RawData TCGA Assembler READ__jhu usc edu__humanmethylation27__Jan 30 2014 txt outputFileName READ _humanmethylation27 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Extract methylation data of primary solid tumor samples ExtractedData__ TP ExtractTissueSpecificSamples inputData Methylation27DataSData tissueType TP singleSampleFlag FALSE sampleTypeFile SupportingFiles TCGASampleType txt Extract methylation data of primary solid tumor samples and solid tissue normal samples ExtractedData__TP_NT ExtractTissueSpecificSamples inputData Methylation27DataSData tissueType c TP NT singleSampleFlag TRUE 26 This function combines two methylation datasets together by doing the following 1 Identify the CpG sites that appear in both datasets and combine the data of these CpG sites 2 Perform quantile normalization on the combined data 3 Draw and save a box plot of the combined data before and after normalization for quality control purpose The picture file names are composed of outputFileName and __ BeforeNormalizationBoxplot png or _AfterNormalizationBoxpl
51. ot png 4 Save the normalized combined data as a tab delimited Gr file The first four columns are Illumina ID of CpG site gene symbol chromosome ID and genomic coordinate The other columns are data of individual samples The first row gives TCGA barcodes of samples refer to https wiki nci nih gov display TCGA TCGA barcode 5 Save the normalized combined data as an R data file rda that includes two variables The first variable is Des which is a character matrix including the four column description of CpG sites It serves as the description of the second variable Data which is a numeric matrix Each column in the matrix corresponds to a sample and the column names are TCGA barcodes of samples The output txt file and rda file contain the same data Having the same data in two different file formats is for the convenience of using data under different software environments Input arguments input a list object containing a methylation dataset to be merged It is a list of two variables One variable is Des which is a four column character matrix including Illumina ID of CpG site gene symbol chromosome ID and genomic coordinate The other variable is Data a numeric matrix containing methylation data Each column in Data corresponds to a sample with column names showing the TCGA barcodes of samples Des serves as the description of Data This list object of input data can be generated by the ProcessMethylation27 Data Proc
52. pleData ProcessedData TCGA Assembler dataType GeneExp verType RNASeqv2 Download and process RPPA protein expression data of six READ patient samples RPPARawData DownloadRPPAData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform mda_rppa_core inputPatientIDs c TCGA EI 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG 3582 01 TCGA AG 4001 01 RPPAData ProcessRPPADataWithGeneAnnotation inputFilePath UserManualExampleData RawData TCGA Assembler READ__mdanderson org__mda_rppa_core__Jan 30 2014 txt outputFileName READ _mda_rppa_core outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Put multi modal data in a vector of list objects to be inputted into CombineMultiPlatformData function inputDataList vector list 5 inputDataList 1 list Des GeneExpDataSDes Data GeneExpDataSData dataType GeneExp inputDataList 2 list Des Methylation4S50_TSS1500_DHSSDes Data Methylation450_TSS1500_DHSSData dataType Methylation inputDataList 3 list Des GeneLevelCNASDes Data GeneLevelCNASData dataType CNA inputDataList 4 list Des RPPADataSDes Data RPPADataSData dataType ProteinExp inputDataList 5 list Des miRNASeqDataSDes Data miRNASeqDataSData dataType miRNAExp Merg
53. ples include tumors their matched normal tissues and control samples if exist The function downloads the data files of individual samples and combines them into tab delimited txt files Input arguments traverseResultFile a character string The path of the directory traverse result file that includes the URLs of all open access data files on TCGA server saveFolderName a character string The path of the directory to save the acquired data files cancerType a character string indicating the cancer type for which to download data Options include ACC BLCA BRCA CESC COAD DLBC ESCA GBM HNSC KICH KIRC KIRP LAML LGG LIHC LUAD LUSC OV PAAD PRAD READ SARC SKCM STAD THCA UCEC UCS Look at https tcga data nci nih gov tcga for information about cancer types assayPlatform a character string indicating the assay platform used to generate the data Currently the only option allowed also be default is genome_wide_snp_6 which indicates Affymetrix Genome Wide Human SNP Array 6 0 In TCGA Genome Wide Human SNP Array 6 0 provides the most abundant copy number data inputPatientIDs a character vector that includes TCGA barcodes of the patients samples the data of which should be obtained If it is NULL by default data of all samples in the specified cancer category will be acquired Barcodes in inputPatientIDs must start with TCGA but do not need to be full length and complete because string matching for iden
54. process miRNA seq data of six READ patient samples miRNASeqRawData DownloadmiRNASeqData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform miRNASeq inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AF 2689 11 TCGA AF 2691 11 23 miRNASeqData ProcessmiRNASeqData inputFilePath UserManualExampleData RawData TCGA Assembler READ__bcgsc ca__illuminahiseq_mirnaseq__NCBI36__Jan 30 2014 txt outputFileName READ illuminahiseq_mirnaseq outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Download and process normalized gene expression data of six READ patient samples RNASeqRawData DownloadRNASeqData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform RNASeqV2 dataType rsem genes normalized_results inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG 3732 11 TCGA AG 3742 11 GeneExpData ProcessRNASeqData inputFilePath UserManualExampleData RawData TCGA Assembler READ__unc edu_illuminahiseq_rnaseqv2__rsem genes normalized_results _Jan 30 2014 txt outputFileName READ illuminahiseq_rnaseqv2__GeneExp outputFileFolder UserManualExam
55. ring to form the names of output data files and box plot picture file outputFileFolder a character string indicating the path of the directory to which the output files will be saved Output argument A list object of two matrix variables The first variable is Des which is a character matrix including two columns i e gene symbol and protein antibody name It serves as the description of the second variable Data which is a numeric matrix Each column in the data matrix is a sample and the column names are TCGA sample barcodes Note Before applying the function check the input data file to see whether gene symbols corresponding to the same protein antibody are separated by a single white space Sometimes the gene symbols are not correctly separated due to errors inherited from the original TCGA data files Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions 39 source Module_B r Load Module B functions Download RPPA protein expression data of six rectum adenocarcinoma READ patient samples and save the acquired data in UserManualExampleData RawData TCGA Assembler RPPARawData DownloadRPPAData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform md
56. tatic Tumor TAM Additional Metastatic Tumor THOC Human Tumor Original Cells Tumor TBM Primary Blood Derived Cancer Bone Marrow Tumor NB Blood Derived Normal Normal NT Solid Tissue Normal Normal NBC Buccal Cell Normal Normal NEBV EBV Immortalized Normal Normal NBM Bone Marrow Normal Normal singleSampleFlag a logical variable If it is TRUE when there are multiple samples of the same patient and the same tissue type only one sample is kept if it is FALSE all samples are kept sampleTypeFile a character string indicating the path of the TCGA sample type file to be used by the function which is TCGASampleType txt in the SupportingFiles folder in the package Output argument A numeric matrix containing the extracted data Each column in the matrix is a sample and each row is a genomic feature The column names of the matrix are the TCGA barcodes of samples Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions 25 source Module_B r Load Module B functions Download humanmethylation27 data of six rectum adenocarcinoma READ patient samples Methylation27RawData DownloadMethylationData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform humanmethylati
57. the data in different software environments Input arguments inputFilePath a character string indicating the path of the input miRNAseq data file acquired by TCGA Assembler module A or downloaded from Firehose website outputFileName a character string to form the names of output data files outputFileFolder a character string indicating the directory to which the output files will be saved fileSource a character string that can be either TCGA Assembler or Firehose TCGA Assembler which is the default setting indicates that the input data file was acquired by TCGA Assembler Module A and Firehose indicates that the input data file was downloaded from Firehose website Output argument A list object of two variables Des and Data Des is a single column character matrix including miRNA names It serves as the description of the second variable Data which is a numeric matrix of RPM values Each column in Data corresponds to a sample and each row corresponds to a miRNA And the column names are TCGA sample barcodes Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions source Module_B r Load Module B functions Download miRNA seq data of six rectum adenocarcinoma READ patient samples 35 miRNASeqRawData DownloadmiRNASeqData traverseResultFile DirectoryTraverseResult_J
58. the second row indicates whether a column is read count or reads per million miRNA reads mapped The first column gives miRNA names And starting from the second column two columns correspond to one sample Examples 10 The present working directory of R must be TCGA Assembler i e the package folder for running the examples source Module_A r Load Module A functions Acquire miRNASeq data of six rectum adenocarcinoma READ patient samples READ_miRNASeqRawData DownloadmiRNASeqData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform miRNASeq inputPatientIDs c TCGA El 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AF 2689 11 TCGA AF 2691 11 Acquire miRNASeq data of all bladder urothelial carcinoma BLCA patient samples BLCA_miRNASeqRawData DownloadmiRNASeqData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType BLCA assayPlatform miRNASeq 11 DownloadRNASeqData lt function traverseResultFile saveFolderName cancerType assayPlatform dataType inputPatientIDs NULL outputFileName This function downloads RNASeq data of specified cancer type generated by specified assay pipeline It downloads the data files of individual samples and combines them
59. thylation27Data inputFilePath UserManualExampleData RawData TCGA Assembler READ__jhu usc edu__humanmethylation27__Jan 30 2014 txt outputFileName READ humanmethylation27 outputFileFolder UserManualExampleData ProcessedData TCGA Assembler Process READ HumanMethylation27 data downloaded from Firehose website and save the results to UserManualExampleData ProcessedData Firehose Methylation27Data ProcessMethylation27Data inputFilePath UserManualExampleData RawData Firehose READ methylation _humanmethylation27__jhu_usc_edu_ _Level_3__within_bioassay_data_set_function__data data txt outputFileName READ _humanmethylation27 outputFileFolder UserManualExampleData ProcessedData Firehose fileSource Firehose 32 ProcessMethylation450Data lt function inputFilePath outputFileName outputFileFolder fileSource TCGA Assembler This function processes HumanMethylation450 BeadChip data file either acquired by TCGA Assembler Module A or downloaded from Firehose website and imports the data into R It does the following 1 For HumanMethylation450 data file downloaded from Firehose website remove redundant columns in the data Firehose HumanMethylation450 data file includes replicated columns of probe descriptions i e gene symbol chromosome ID genomic coordinate which are identical for each sample This redundant information makes the file size very large more than 10GB for some cancer types wh
60. tifying the samples data starts from the beginning of the barcodes For details of TCGA barcodes refer to https wiki nci nih gov display TCGA TCGA barcode outputFileName a character string used to form the names of obtained data files It is the empty string by default Output arguments A list object of four character matrices containing the data and their descriptions retrieved from TCGA DCC Refer to the output data file section for introduction of the contents in the character matrices Output data files The DownloadCNAData function generates four tab delimited txt data files The file names consist of six components 1 outputFileName 2 cancer type 3 institution that generated the data which is broad mit edu 4 assay platform used to generate the data which is genome_wide_snp_6 5 data type 6 the date on which the input directory traverse result file was generated Double underscore __ is used to separate the six components in the file name If outputFileName is an empty string the file names consist of only the other five components The file names of the four data files differ in component 5 data type which can be hg18 hg19 nocnv_hg18 nocnv_hg19 hg18 and hg19 indicate that in preparation for segmentation the probes are sorted based on the order of reference genome hg18 and hg19 respectively nocnv indicates that a fixed set of probes that frequently contain germline CNVs are removed prior to segmentation
61. tion downloads RPPA protein expression data of specified cancer type It downloads the data files of individual samples and combines them into data matrix format The samples to be acquired include tumors their matched normal tissues and control samples if exist Input arguments traverseResultFile a character string The path of the directory traverse result file that includes the URLs of all open access data files on TCGA server saveFolderName a character string The path of the directory to save the acquired data matrix files cancerType a character string The cancer type for which to download data Options include ACC BLCA BRCA CESC COAD DLBC ESCA GBM HNSC KICH KIRC KIRP LAML LGG LIHC LUAD LUSC OV PAAD PRAD READ SARC SKCM STAD THCA UCEC UCS Look at https tcga data nci nih gov tcga for information about cancer types assayPlatform a character string indicating the assay platform used to generate the data It must be mda_rppa_core which is also the default value inputPatientIDs a character vector that includes TCGA barcodes of the patients samples whose data should be obtained If it is NULL by default data of all samples in the specified cancer category will be acquired Barcodes in inputPatientIDs must start with TCGA but do not need to be full length and complete because string matching for identifying the samples data starts from the beginning of the barcodes For details of TCGA barcodes re
62. unc edu_READ IlluminaHiSeq_RNASeqV2 mage tab 1 6 0 DESCRIPTION txt Examples The present working directory of R must be TCGA Assembler i e the package folder for running the examples rm list Is Clear workspace source Module_A r Load Module A functions Acquire normalized gene expression data and exon expression data of six rectum adenocarcinoma READ patient samples produced by RNASeqV2 pipeline READ_RNASeqV2RawData DownloadRNASeqData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform RNASeqV2 dataType c rsem genes normalized_results exon_quantification inputPatientIDs c TCGA EI 6884 01 TCGA DC 5869 01 TCGA G5 6572 01 TCGA F5 6812 01 TCGA AG 3732 11 TCGA AG 3742 11 Acquire gene expression data and splice junction expression data of all READ patient samples produced by RNASeqV1 pipeline READ_RNASeqV1RawData DownloadRNASeqData traverseResultFile DirectoryTraverseResult_Jan 30 2014 rda saveFolderName UserManualExampleData RawData TCGA Assembler cancerType READ assayPlatform RNASeqV1 dataType c gene quantification spljxn quantification 13 DownloadRPPAData lt function traverseResultFile saveFolderName cancerType assayPlatform mda_rppa_core inputPatientIDs NULL outputFileName This func
63. vector that includes TCGA barcodes of the patients samples the data of which should be obtained If it is NULL by default data of all samples in the specified cancer category will be acquired Barcodes in inputPatientIDs must start with TCGA but do not need to be full length and complete because string matching for identifying the samples data starts from the beginning of the barcodes For details of TCGA barcodes refer to https wiki nci nih gov display TCGA TCGA barcode outputFileName a character string used to form the names of obtained data files It is the empty string by default Output arguments A character matrix containing the data and their descriptions retrieved from TCGA DCC Refer to the description of output data file for introduction of the content in the character matrix Output data files The name of the output data file consists of five components 1 outputFileName 2 cancer type 3 institution that generated the data i e jhu usc edu 4 assay platform used to generate the data i e humanmethylation27 or humanmethylation450 5 the date on which the input directory traverse result file was generated Double underscore __ is used to separate the five components in the file name If outputFileName is an empty string the file name consists of only the other four components The output data file is a tab delimited txt file In the file the first column includes the indices that Illumina gives to CpG sites
64. x plot of the obtained single value methylation data The file name of the box plot picture is composed of outputFileName regionOption DHSOption and boxplot png with double underscore __ separating them 3 Save the single value methylation data as a tab delimited txt file The first two columns are gene symbol and the single value type that shows the regionOption and DHSOption used to calculate the data with in between to separate them The other columns are data of individual samples The first row gives TCGA barcodes of samples refer to https wiki nci nih gov display TCGA TCGA barcode The name of the file is composed of outputFileName regionOption and DHSOption with double underscore __ separating them 4 KEN Save the single value methylation data as an R data file rda that includes two variables The first variable is Des which is a two column character matrix including gene symbol and the single value type that shows the regionOption and DHSOption used to calculate the data with in between to separate them Des serves as the description of the second variable Data which is a numeric matrix Each column in Data is a sample and each row corresponds to a gene The column names of Data are TCGA barcodes of samples The name of the file is composed of outputFileName regionOption and DHSOption with double underscore __ separating them The output txt file and rda file contain the same data Having the sa

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