R/rna.peaks.to.genome.R

In helen-zhu/ConsensusPeaks: A Method for Peak Merging And Distribution Fitting Across Biological Replicates

.rna.peaks.to.genome = function(merged.peaks.rna, geneinfo){

  # Return an empty GRanges if no peaks survive
  if(length(merged.peaks.rna) == 0){
    return(GenomicRanges::GRanges())
  }

  # Transferring to Genomic Coordinates
  merged.peaks.genome = merged.peaks.rna
  GenomicRanges::end(merged.peaks.genome) = geneinfo$RNA2DNA[GenomicRanges::end(merged.peaks.genome)]
  GenomicRanges::start(merged.peaks.genome) = geneinfo$RNA2DNA[GenomicRanges::start(merged.peaks.genome)]

  # Creating a GRanges object from the Annotation
  anno_gr = GenomicRanges::makeGRangesFromDataFrame(geneinfo$anno)

  # Filtering Out Introns
  merged.peaks.filtered.genome = GenomicRanges::GRanges()
  for(i in 1:length(merged.peaks.genome)){
    tmp.gr = GenomicRanges::intersect(merged.peaks.genome[i], anno_gr)
    if(length(tmp.gr) > 0){S4Vectors::mcols(tmp.gr) = S4Vectors::mcols(merged.peaks.genome[i])}
    merged.peaks.filtered.genome = c(merged.peaks.filtered.genome, tmp.gr)
  }

  return(merged.peaks.filtered.genome)
}