## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- library(knitr) opts_chunk$set(comment="", message=FALSE, warning = FALSE, tidy.opts=list(keep.blank.line=TRUE, width.cutoff=150),options(width=150), eval = FALSE) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("RTCGA") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # if (!require(devtools)) { # install.packages("devtools") # require(devtools) # } # BiocManager::install("RTCGA/RTCGA") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # browseVignettes("RTCGA") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # library(RTCGA) # checkTCGA('Dates') ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # (cohorts <- infoTCGA() %>% # rownames() %>% # sub("-counts", "", x=.)) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # #dir.create( "data/CNV2" ) # releaseDate <- "2015-11-01" # for (cohort in cohorts) { # try(downloadTCGA( cancerTypes = cohort, destDir = "data/CNV2", date = releaseDate, dataSet = "Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3" ), # silent=TRUE) # } ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # allCNVFiles <- list.files("data/CNV2", pattern = "cnv", recursive = TRUE, full.names = TRUE) # for (CNVFile in allCNVFiles) { # CNV <- read.table(CNVFile,h=T) # # cohortName <- strsplit(strsplit(CNVFile, split = "/")[[1]][4], "\\.")[[1]][1] # name = paste0(cohortName, ".CNV") # assign(name, CNV) # save(list = name, file=paste0("data/CNV2/", name, ".rda"), compression_level = 9, compress = "xz") # # } #