R/utils.R

In CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

# Constants: color schema used for plotting CNVs with CopyNumberPlots package
CNV_COLORS <- c("0" = "black", "#A5C94D", "gray", "#C2506A","black","black","black","black")
CONFIRM_COLOR <- "#3179B1"
DISCARD_COLOR <- "#F28834"
NEUTRAL_COLOR <- "#555555"

#' auxAddCNcolumn
#'
#' @description
#' Adds a 'cn' column to the \code{cnvs.gr} data.frame or GRanges.
#'
#' @details
#' For each row, \code{cn} column is filled with 1 if \code{cnv} is "deletion", 3 if \code{cnv} is "duplication"
#'
#' @param cnvs.gr \code{data.frame or GRanges} containing the column 'cnv' with "deletion" or "duplication" as values
#'
#'
#' @return
#' input \code{cnvs.gr} with the new column 'cn'
#'
#' @import assertthat
#' @importFrom methods is
#'
auxAddCNcolumn <- function(cnvs.gr){

  assertthat::assert_that(methods::is(cnvs.gr, "GRanges") || is.data.frame(cnvs.gr))

  cnvs.gr$cn <- 0
  if (length(cnvs.gr[cnvs.gr$cnv == "deletion"]) > 0) {
    cnvs.gr[cnvs.gr$cnv == "deletion"]$cn <- 1
  }
  if (length(cnvs.gr[cnvs.gr$cnv == "duplication"]) > 0){
    cnvs.gr[cnvs.gr$cnv == "duplication"]$cn <- 3
  }
  return (cnvs.gr)
}