R/segment_varbin.R

In whtns/varbintools: Sequence Based Copy Number Detection Using Variable Bin Lengths

#' Segment Varbin
#'
#' @param dat
#'
#' @return
#' @export
#'
#' @examples
segment_varbin <- function(dat) {
  dat$loess.ratio[which(dat$loess.ratio == 0)] <- 1e-3
  dat$chrom <- as.numeric(dat$chrom)

  # creating a CNA object
  CNA.object <- DNAcopy::CNA(log(dat$loess.ratio, base=2), dat$chrom, dat$chrompos, data.type="logratio",
                             sampleid="dat")

  # smoothing outliers
  smoothed.CNA.object <- DNAcopy::smooth.CNA(CNA.object)

  # segmenting with CBS
  segment.smoothed.CNA.object <- DNAcopy::segment(smoothed.CNA.object,
                                                  alpha=0.01,
                                                  min.width=5,
                                                  undo.splits="prune",
                                                  undo.prune=0.05)

  dat$seg.mean.loess <- rep(2^segment.smoothed.CNA.object$output$seg.mean,
                             segment.smoothed.CNA.object$output$num.mark)

  return(dat)
}