## ---- 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------------------------------------------------------------------------------------------------------------------------------------
#  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( "data2" )
#  releaseDate <- "2015-11-01"
#  sapply(cohorts,
#  			 function(element){
#  			 	try({
#  downloadTCGA( cancerTypes = element,
#                dataSet = "Merge_methylation__humanmethylation27",
#                destDir = "data2",
#                date = releaseDate )
#  				})
#  })

## ---- 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 = "_"),
#                           ".methylation.path"),
#                envir = .GlobalEnv)
#     })

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

## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------
#  OV.methylation[1:300,] -> OV.methylation1
#  OV.methylation[301:612,] -> OV.methylation2
#  rm(OV.methylation)
#  grep( "methylation", 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.methylation,COAD.methylation,
#     									 COADREAD.methylation,GBMLGG.methylation,
#     									 GBM.methylation,KIPAN.methylation,
#     									 KIRC.methylation,KIRP.methylation,
#     									 LAML.methylation,LUAD.methylation,
#     									 LUSC.methylation,OV.methylation1,OV.methylation2,
#     									 READ.methylation,STAD.methylation,
#     									 STES.methylation,UCEC.methylation,
#                       # overwrite = TRUE,
#                        compress="xz")