R/pre_process.R

In izarvillasante/SCNA: What the Package Does (One Line, Title Case)

pre_process<-function(ss,subf,purity=T,query=T,out="analysis/ChAMP/"){
  ##Create dir ChAMP/n/. put all the sample sheet idat files here
  ChAMP_folder<-paste0(out,subf)
  #ChAMP_folder<-paste(getwd(),ChAMP_folder,sep="/")

  dir.create(ChAMP_folder)
  ## this directory, you should copy the file "Sample_Sheet.csv", as ChAMP will look for it.
  message("working directory: ",ChAMP_folder)
  file.remove(list.files(ChAMP_folder, full.names = TRUE))
  file.copy(paste0(ss$filenames,"_Grn.idat"),ChAMP_folder)
  file.copy(paste0(ss$filenames,"_Red.idat"),ChAMP_folder)
  message(ss$Basename)

  write.csv(ss,paste0(ChAMP_folder,"/Sample_sheet.csv"))
  data(hm450.manifest.hg19 )
  #Run ChAMP with method for QC minfi
  myLoad <- ChAMP::champ.load(ChAMP_folder, method="minfi")
  #read.metharray.exp(base = ChAMP_folder)->a
  ss<-myLoad$pd
  #save(myLoad,file = paste0(ChAMP_folder,"TCGA_New.RData"))#Give it the name you want.
  message("Champ does load data")
  if(purity==T){
    purity<-purify(myLoad=myLoad)
    message("Rfpurifies")
    ss$Purity_Impute_RFPurity.Absolute. <- purity
    write.table(ss,paste(ChAMP_folder,"Sample_Sheet.txt",sep="/"), col.names = T, row.names = F, quote = F, sep="\t")
    message(paste("ss is saved ",subf))
  }
  if(query==T){
    query <- queryfy(myLoad$rgSet,ss=ss,ChAMP_folder=ChAMP_folder)
    saveRDS(query,paste0(ChAMP_folder,"/intensities.rds"),compress = FALSE)
    message("Pre-processing Completed successfully!")
    return(query)
  }
}