## ---- 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")
#  
#  }
#