R/segToGr.R

In ttriche/biscuitEater: a bunch of convenience functions for Biscuit

#' reverse a grToSeg... import a segmentation file
#' 
#' @param seg       the .seg filename
#' @param genome    genome against which segments were annotated ("hg19")
#' @param name      .seg file column to use as $name metadata ("ID")
#' @param score     .seg file column to use as $score metadata ("seg.mean")
#' 
#' @return          a GRanges
#'
#' @import GenomicRanges
#'
#' @export
segToGr <- function(seg, genome="hg19", name="ID", score="seg.mean") { 
  segs <- read.table(seg, header=TRUE, sep="\t")
  names(segs) <- base::sub(name, "name", names(segs))
  names(segs) <- base::sub(score, "score", names(segs))
  firstTwo <- c("score", "name")
  segs <- segs[, c(firstTwo, setdiff(names(segs), firstTwo))]
  if (nrow(segs) > 0) {
    gr <- sort(makeGRangesFromDataFrame(segs, keep=TRUE))
    names(gr) <- gr$name
    return(gr)
  } else { 
    return(GRanges())
  }
}