patrick-edu / prad

RNA

PRAD

source("http://bioconductor.org/bioClite.R") biocLite() biocLite("RTCGAToolbox") biocLite("devtools") biocLite("PGSEA") biocLite("GSEABase") biocLite("pathview") library(page) library(PSEA) library(RTCGAToolbox) library(BiocInstaller) library(devtools) library(DESeq2) if(require(RTCGAToolbox)){ si <- devtools::session_info() must.install <- FALSE if(!grepl("link-ny", si$packages[si$packages[, 1] == "RTCGAToolbox", 5], ignore.case = TRUE)){ must.install <- TRUE } }else{ must.install <- TRUE } if(must.install){ biocLite(c("limma", "RCircos", "data.table", "RCurl", "RJSONIO")) biocLite("Link-NY/RTCGAToolbox", "vjcitn/MultiAssayExperiment") }

library(RTCGAToolbox) rundates <- getFirehoseRunningDates() analysisdates <- getFirehoseAnalyzeDates() prad <- getFirehoseData("PRAD", runDate=rundates[1], gistic2_Date=analysisdates[1], 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)

choices <- tolower(gsub("_", "", c("RNAseq_Gene", "miRNASeq_Gene", "RNAseq2_Gene_Norm", "CNA_SNP", "CNV_SNP", "CNA_Seq", "CNA_CGH", "Methylation", "Mutation", "mRNA_Array", "miRNA_Array", "RPPA")))

dses <- lapply(choices, function(choice) try(extract(prad, choice, clinic=TRUE), silent=TRUE)) names(dses) <- choices dses

set.rnaseq <- extract(prad, "rnaseq2genenorm") write.csv(exprs(eset.rnaseq), file="prad_rnaseq.csv") write.csv(pData(eset.rnaseq), file="prad_clinical.csv") saveRDS(eset.rnaseq, file="prad_eset.rds")

eset.rnaseq <- readRDS("prad_eset.rds") hist(exprs(eset.rnaseq["KLK3", ])) hist(log(exprs(eset.rnaseq["KLK3", ])))