## ---- 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)
#  }
#  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"
#  
#  # data produced with Illumina Genome Analyzer machine
#  sapply( cohorts, function(element){
#  tryCatch({
#  downloadTCGA( cancerTypes = element,
#                dataSet = "Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3",
#                destDir = "data2",
#                date = releaseDate )},
#  error = function(cond){
#     cat("Error: Maybe there weren't mutations data for ", element, " cancer.\n")
#  }
#  )
#  })
#  
#  # data produced with Illumina HiSeq 2000 machine
#  sapply( cohorts, function(element){
#  tryCatch({
#  downloadTCGA( cancerTypes = element,
#                dataSet = "Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__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=70))

## ---- 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()
#        })

## ---------------------------------------------------------------------------------------------------------------------------------------------------
#  data2_files <- list.files("data2")
#  
#  # Paths to data produced with Illumina Genome Analyzer machine
#  illuminaga <- which(grepl("illuminaga", x = data2_files))
#  data2_files[illuminaga] %>%
#     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 = "_"),
#                              ".miRNASeq_illuminaga.path"),
#                   envir = .GlobalEnv)
#        })
#  # Paths to data produced with Illumina HiSeq 2000 machine
#  data2_files[-illuminaga] %>%
#     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 = "_"),
#                           ".miRNASeq_illuminahiseq.path"),
#                   envir = .GlobalEnv)
#        })

## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------
#  path_vector <- ls() %>%
#     grep("miRNASeq.*path", x = ., value = TRUE)
#  # First we will read miRNASeq data produced by both Illumina Genome Analyzer and
#  # Illumina HiSeq 2000 machines
#  path_vector %>%
#     sapply(function(element){
#        tryCatch({
#           readTCGA(get(element, envir = .GlobalEnv),
#                 dataType = "miRNASeq") %>%
#           assign(value = .,
#                  x = sub("\\.path", "", x = element),
#                  envir = .GlobalEnv )
#        }, error = function(cond){
#           cat(element)
#        })
#       invisible(NULL)
#      }
#  )
#  
#  # Now we will add special column `machine` to miRNASeq data depending on
#  # kind of machine which produced data
#  sapply(cohorts, function(element){
#     w <- grep(paste0("^",element, "\\."), x = path_vector, value = TRUE)
#     if (length(w) == 0) {
#        invisible(NULL)
#     } else if ((length(w) == 1) && grepl("illuminaga", x = w)){
#        data <- get(paste0(element,".miRNASeq_illuminaga"), envir = .GlobalEnv)
#        data <- cbind(machine = "Illumina Genome Analyzer", data)
#     } else if ((length(w) == 1) && grepl("illuminahiseq", x = w)){
#        data <- get(paste0(element,".miRNASeq_illuminahiseq"), envir = .GlobalEnv)
#        data <- cbind(machine = "Illumina HiSeq 2000", data)
#     } else if ((length(w) == 2) && grepl("illuminaga|illuminahiseq", x=w[1]) && grepl("illuminaga|illuminahiseq", x=w[2])){
#        data_illuminaga <- get(paste0(element,".miRNASeq_illuminaga"), envir = .GlobalEnv)
#        data_illuminaga <- cbind(machine = "Illumina Genome Analyzer", data_illuminaga)
#        data_illuminahiseq <- get(paste0(element,".miRNASeq_illuminahiseq"), envir = .GlobalEnv)
#        data_illuminahiseq <- cbind(machine = "Illumina HiSeq 2000", data_illuminahiseq)
#        data <- rbind(data_illuminaga, data_illuminahiseq)
#     }
#     assign(value = data, x = paste0(element, ".miRNASeq"), envir = .GlobalEnv )
#     invisible(NULL)
#  })
#  

## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------
#  grep( "miRNASeq", x=ls(), value = TRUE) %>%
#     grep("illuminahiseq|illuminaga", 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(ACC.miRNASeq,BLCA.miRNASeq,BRCA.miRNASeq,CESC.miRNASeq,
#                        CHOL.miRNASeq,COAD.miRNASeq,COADREAD.miRNASeq,DLBC.miRNASeq,
#                        ESCA.miRNASeq,FPPP.miRNASeq,GBM.miRNASeq,GBMLGG.miRNASeq,
#                        HNSC.miRNASeq,KICH.miRNASeq,KIPAN.miRNASeq,KIRC.miRNASeq,
#                        KIRP.miRNASeq,LAML.miRNASeq,LGG.miRNASeq,LIHC.miRNASeq,
#                        LUAD.miRNASeq,LUSC.miRNASeq,MESO.miRNASeq,OV.miRNASeq,
#                        PAAD.miRNASeq,PCPG.miRNASeq,PRAD.miRNASeq,READ.miRNASeq,
#                        SARC.miRNASeq,SKCM.miRNASeq,STAD.miRNASeq,STES.miRNASeq,
#                        TGCT.miRNASeq,THCA.miRNASeq,THYM.miRNASeq,UCEC.miRNASeq,
#                        UCS.miRNASeq,UVM.miRNASeq,
#                        overwrite = TRUE,
#                        compress="xz")