R/getGRangesFormat.r

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

getGRangesFormat <- function(segments) {
  nc <- ncol(segments)
  if (!is.multiseg(segments)) {
    gr <- GRanges(
      seqnames = segments$chrom,
      ranges = IRanges(start = segments$start.pos, end = segments$end.pos, names = segments$sampleID)
    )
    mcols(gr) <- DataFrame(segments[, c(3, 6:nc)])
  } else {
    gr <- GRanges(
      seqnames = segments$chrom,
      ranges = IRanges(start = segments$start.pos, end = segments$end.pos)
    )
    mcols(gr) <- DataFrame(segments[, c(2, 5:nc)])
  }

  return(gr)
}