R/tile_bins.R

In trichelab/spiky: Spike-in calibration for cell-free MeDIP

#' Tile the assembly-based contigs of a merged assembly/spike GRanges.
#'
#' refactored out of scan_spiked_bam for more explicit information flow
#'
#' @param gr          the GRanges
#' @param binwidth    bin width to tile (default is 300)
#'
#' @return            a GRanges of bins
#'
#' @examples
#'
#' bam <- system.file("extdata", "ex1.bam", package="Rsamtools",
#'                    mustWork=TRUE)
#' gr <- as(seqinfo_from_header(bam), "GRanges")
#' genome(gr) <- "notspike"
#' tile_bins(gr)
#'
#'
#' @export
tile_bins <- function(gr, binwidth=300L) {

  chroms <- subset(seqlevels(gr), genome(gr)[seqlevels(gr)] != "spike" )
  si <- seqinfo(gr)[chroms]
  message("Tiling ", binwidth, "bp bins across the genome...", appendLF=FALSE)
  bins <- tileGenome(si, tilewidth=binwidth, cut.last.tile.in.chrom=TRUE)
  message("Done.")
  return(bins)

}