Obtaining TCGA data

Downloading TCGA data and obtaining bioconductor classes

Install Bioconductor dependencies, download and install RTCGAToolbox package fork, and download TCGA datasets

source("http://bioconductor.org/biocLite.R")
biocLite()

BiocInstaller::biocLite("LiNk-NY/RTCGAToolbox")
library(RTCGAToolbox)

getFirehoseRunningDates(last=5)
getFirehoseAnalyzeDates(last=5)

ov <- getFirehoseData("OV", runDate="20150402", gistic2_Date="20141017", RNAseq_Gene=TRUE, 
          miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP=TRUE, CNV_SNP=TRUE, CNA_Seq=TRUE, 
          CNA_CGH=TRUE,  Methylation=TRUE, Mutation=TRUE, mRNA_Array=TRUE, miRNA_Array=TRUE, 
          RPPA=TRUE, destdir = ".")

gbm <- getFirehoseData("GBM", runDate="20150402", gistic2_Date="20141017", RNAseq_Gene=TRUE, 
          miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP=TRUE, CNV_SNP=TRUE, CNA_Seq=TRUE, 
          CNA_CGH=TRUE,  Methylation=TRUE, Mutation=TRUE, mRNA_Array=TRUE, miRNA_Array = TRUE,  
          RPPA=TRUE, destdir = ".")

coad <- getFirehoseData("COAD", runDate="20150402", gistic2_Date="20141017", RNAseq_Gene=TRUE, 
          miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP = TRUE, CNV_SNP=TRUE, CNA_Seq = TRUE, 
          CNA_CGH = TRUE, Methylation = TRUE, Mutation = TRUE, mRNA_Array = TRUE, miRNA_Array = TRUE, 
          RPPA = TRUE, destdir = ".")

laml <- getFirehoseData("LAML", runDate="20150402", gistic2_Date="20141017", RNAseq_Gene=TRUE, 
          miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP = TRUE, CNV_SNP=TRUE, CNA_Seq = TRUE, 
          CNA_CGH = TRUE, Methylation = TRUE, Mutation = TRUE, mRNA_Array = TRUE, miRNA_Array = TRUE, 
          RPPA = TRUE, destdir = ".")

blca <- getFirehoseData("BLCA", runDate="20150402", gistic2_Date="20141017", RNAseq_Gene=TRUE, 
          miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP = TRUE, CNV_SNP=TRUE, CNA_Seq = TRUE, 
          CNA_CGH = TRUE, Methylation = TRUE, Mutation = TRUE, mRNA_Array = TRUE, miRNA_Array = TRUE, 
          RPPA = TRUE, destdir = ".")

R Objects can be saved to an .Rda file

save(ov, file = "~/Documents/SupportTCGA/ov.Rda")
save(gbm, file = "~/Documents/SupportTCGA/gbm.Rda")
save(coad, file = "~/Documents/SupportTCGA/coad.Rda")
save(laml, file = "~/Documents/SupportTCGA/laml.Rda")
save(blca, file = "~/Documents/SupportTCGA/blca.Rda")

Extract data as a Bioconductor GenomicRanges object

bcOV <- extract(ov, "cnasnp", clinical=TRUE)
bcOV