R/LabelGenomecov.R

In afrangou/CleanCNA: Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.

# -------------------------- #
# Label bedtools_genomecov files with type of CNA
# -------------------------- #

#' @name
#' LabelGenomecov
#'
#' @title
#' Collate all segments in all samples in the cohort
#'
#' @description
#' Label bedtools_genomecov files with type of CNA
#'
#' @param
#' filestub = dir (with trailling slash) containing *regions_normalised_out files for all cna types
#' segfile_name = label of cohort, eg 'TGCT'
#'
#' @return
#' writes same name file with cna types labelled
#'

# collate all segments in subclones files across cohort
LabelGenomecov <- function(filestub,segfile_name) {
  # label each of these files with the copy number type
  cnas = c("homdel","loh","otherloss","nochange","gain","biggain")
  for (i in 1:length(cnas)) {
    file = read.table(paste0(filestub,segfile_name,"_",cnas[i],"_regions.out"),
                      sep="\t",
                      stringsAsFactors=F)
    file = cbind(file,cnas[i])
    write.table(file,paste0(filestub,segfile_name,"_",cnas[i],"_regions.out"),
                sep="\t",
                col.names=F,
                row.names=F,
                quote=F)
  }
}