## ---- 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)
#  }
#  biocLite("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" ) # name of a directory in which data will be stored
#  releaseDate <- "2015-11-01"
#  sapply( cohorts, function(element){
#  tryCatch({
#  downloadTCGA( cancerTypes = element,
#                dataSet = "rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level",
#                destDir = "data2",
#                date = releaseDate )},
#  error = function(cond){
#     cat("Error: Maybe there weren't rnaseq 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 = "_"),
#                           ".rnaseq.path"),
#                envir = .GlobalEnv)
#     })

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

## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------
#  grep( "rnaseq", ls(), value = TRUE) %>%
#     grep("path", x=., value = TRUE, invert = TRUE) %>%
#     cat( sep="," ) #can one to it better? as from use_data documentation:
#     # ...	Unquoted names of existing objects to save
#     devtools::use_data(ACC.rnaseq,BLCA.rnaseq,BRCA.rnaseq,
#     									 CESC.rnaseq,CHOL.rnaseq,COADREAD.rnaseq,
#     									 COAD.rnaseq,DLBC.rnaseq,ESCA.rnaseq,
#     									 GBMLGG.rnaseq,GBM.rnaseq,HNSC.rnaseq,
#     									 KICH.rnaseq,KIPAN.rnaseq,KIRC.rnaseq,
#     									 KIRP.rnaseq,LAML.rnaseq,LGG.rnaseq,
#     									 LIHC.rnaseq,LUAD.rnaseq,LUSC.rnaseq,
#     									 OV.rnaseq,PAAD.rnaseq,PCPG.rnaseq,
#     									 PRAD.rnaseq,READ.rnaseq,SARC.rnaseq,
#     									 SKCM.rnaseq,STAD.rnaseq,STES.rnaseq,
#     									 TGCT.rnaseq,THCA.rnaseq,THYM.rnaseq,
#     									 UCEC.rnaseq,UCS.rnaseq,UVM.rnaseq,
#                       # overwrite = TRUE,
#                        compress="xz")