## ---- 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 = "Mutation_Packager_Calls.Level",
#                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)
#     })

## ---------------------------------------------------------------------------------------------------------------------------------------------------
#  cohorts %>%
#  	sapply(function(element){
#  		grep(paste0("_", element, "\\."),
#  				 x = list.files("data2") %>%
#  				 	file.path("data2", .),
#  				 value = TRUE)
#  		}) -> potential_datasets
#  
#  for(i in seq_along(potential_datasets)){
#  	if(length(potential_datasets[[i]]) > 0){
#  		assign(value =  potential_datasets[[i]],
#  					 x = paste0(names(potential_datasets)[i], ".mutations.path"),
#  					 envir = .GlobalEnv)
#  	}
#  }
#  

## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------
#  ls() %>%
#     grep("mutations\\.path", x = ., value = TRUE) %>%
#     sapply(function(element){
#        tryCatch({
#           readTCGA(get(element, envir = .GlobalEnv),
#                 dataType = "mutations") -> mutations_file
#           	for( i in 1:ncol(mutations_file)){
#  						mutations_file[, i] <- iconv(mutations_file[, i],
#  																				 "UTF-8", "ASCII", sub="")
#  					}
#           	
#           assign(value = mutations_file,
#                  x = sub("\\.path", "", x = element),
#                  envir = .GlobalEnv )
#        }, error = function(cond){
#           cat(element)
#        })
#       invisible(NULL)
#      }
#  )

## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------
#  grep( "mutations", 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.mutations,BLCA.mutations,BRCA.mutations,
#     									 CESC.mutations,CHOL.mutations,COAD.mutations,
#     									 COADREAD.mutations,DLBC.mutations,ESCA.mutations,
#     									 GBMLGG.mutations,GBM.mutations,HNSC.mutations,
#     									 KICH.mutations,KIPAN.mutations,KIRC.mutations,
#     									 KIRP.mutations,LAML.mutations,LGG.mutations,
#     									 LIHC.mutations,LUAD.mutations,LUSC.mutations,
#     									 OV.mutations,PAAD.mutations,PCPG.mutations,
#     									 PRAD.mutations,READ.mutations,SARC.mutations,
#     									 SKCM.mutations,STAD.mutations,STES.mutations,
#     									 TGCT.mutations,THCA.mutations,UCEC.mutations,
#     									 UCS.mutations,UVM.mutations,
#                       # overwrite = TRUE,
#                        compress="xz")