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

## ---- eval=FALSE---------------------------------------------------------
## if (!require(devtools)) {
##     install.packages("devtools")
##     require(devtools)
## }
## install_github("RTCGA/RTCGA")

## ---- eval=FALSE---------------------------------------------------------
## browseVignettes("RTCGA")

## ---- eval=FALSE---------------------------------------------------------
## library(RTCGA)
## checkTCGA('Dates')

## ---- eval=FALSE---------------------------------------------------------
## (cohorts <- infoTCGA() %>%
##    rownames() %>%
##    sub("-counts", "", x=.))

## ---- eval=FALSE---------------------------------------------------------
## # dir.create( "data2" )
## releaseDate <- "2015-11-01"
## sapply( cohorts, function(element){
## tryCatch({
## downloadTCGA( cancerTypes = element,
##               dataSet = "Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3",
##               destDir = "data2",
##               date = releaseDate )},
## error = function(cond){
##    cat("Error: Maybe there weren't mutations data for ", element, " cancer.\n")
## }
## )
## })

## ---- eval=FALSE---------------------------------------------------------
## list.files( "data2") %>%
##    file.path( "data2", .) %>%
##    file.rename( to = substr(.,start=1,stop=50))

## ---- eval=FALSE---------------------------------------------------------
## list.files( "data2") %>%
##    file.path( "data2", .) %>%
##    sapply(function(x){
##       if (x == "data2/NA")
##          file.remove(x)
##    })

## ------------------------------------------------------------------------
list.files( "data2") %>% 
   file.path( "data2", .) %>%
   sapply(function(x){
      file.path(x, list.files(x)) %>%
         grep(pattern = "MANIFEST.txt", x = ., value=TRUE) %>%
         file.remove()
      })

## ------------------------------------------------------------------------

list.files("data2") %>%
   file.path("data2", .) %>%
   sapply(function(y){
      file.path(y, list.files(y)) %>%
      assign( value = .,
              x = paste0(list.files(y) %>%
                            gsub(x = .,
                                 pattern = "\\..*",
                                 replacement = "") %>%
                            gsub(x=., pattern="-", replacement = "_"),
                         ".mRNA.path"),
              envir = .GlobalEnv)
   })

## ---- eval=FALSE---------------------------------------------------------
## ls() %>%
##    grep("mRNA\\.path", x = ., value = TRUE) %>%
##    sapply(function(element){
##       tryCatch({
##          readTCGA(get(element, envir = .GlobalEnv),
##                dataType = "mRNA") %>%
##          assign(value = .,
##                 x = sub("\\.path", "", x = element),
##                 envir = .GlobalEnv )
##       }, error = function(cond){
##          cat(element)
##       })
##      invisible(NULL)
##     }
## )

## ---- eval=FALSE---------------------------------------------------------
## grep( "mRNA", ls(), value = TRUE) %>%
##    grep("path", x=., value = TRUE, invert = TRUE) %>%
##    cat( sep="," ) #can one to id better? as from use_data documentation:
##    # ...	Unquoted names of existing objects to save
##    devtools::use_data(BRCA.mRNA,COAD.mRNA,COADREAD.mRNA,GBMLGG.mRNA,
##                       KIPAN.mRNA,KIRC.mRNA,KIRP.mRNA,LGG.mRNA,LUAD.mRNA,
##                       LUSC.mRNA,OV.mRNA,READ.mRNA,UCEC.mRNA,
##                       overwrite = TRUE,
##                       compress="xz")