a function to split TCGA barcodes

split_tcga_barcode.R

split_tcga_barcode <- function(x, split.char="-"){
  tmp = strsplit(x, split.char)[[1]]
  
  # default values
  s.tss = "NA";
  s.participant = "NA";
  s.programcode = "NA";
  s.nucleic = "NA";
  s.portion = "NA";
  s.sampletype = "00";
  # tooling needs this
  s.portionanalyte = "NA";
  error = 0
  
  # Do some validations as well, TSS - 2 chars, sampletype - 2chars
  s.tss = tmp[2];
  s.participant = tmp[3];
  s.sampletype = substr(tmp[4], 1, 2)
  
  # splitting aliquot and its type DNA RNA...
  tmp2 <- strsplit(gsub("([0-9]*)([A-Z]*)","\\1!\\2",tmp[5]),"!")[[1]]
  
  # extract 
  if(tmp2[2] %in% c("D","G","W","X")){
    s.nucleic <- "DNA"
  }else if(tmp2[2] %in% c("H","R","T")){
    s.nucleic <- "RNA"
  }
  
  s.portion = tmp2[1];
  s.portionanalyte = tmp2[2]

  return(list(sampleid = x, 
              tissuesourcesite = s.tss,
              participant = s.participant,
              sampletype = s.sampletype,
              programcode = s.programcode,
              nucleicacidtype = s.nucleic,
              portion = s.portion,
              portionanalyte = s.portionanalyte,
              error = error))
}