R/matchSeqLevels.R

In fursham-h/ponder:

#' Match seqnames of input GRanges to reference GRanges
#'
#' @param inGRanges GRanges object with seqnames to change
#' @param refGRanges GRanges object from which seqnames is referenced
#'
#' @return Corrected input GRanges
#' @export
#'
matchSeqLevels <- function(inGRanges, refGRanges){
  
  suppressWarnings(
    if (GenomeInfoDb::seqlevelsStyle(inGRanges) != GenomeInfoDb::seqlevelsStyle(refGRanges)) {
      newStyle <- GenomeInfoDb::mapSeqlevels(GenomeInfoDb::seqlevels(inGRanges), GenomeInfoDb::seqlevelsStyle(refGRanges))
      newStyle = newStyle[!is.na(newStyle)]
      inGRanges <- GenomeInfoDb::renameSeqlevels(inGRanges, newStyle)
      
      if (any(!GenomeInfoDb::seqlevels(inGRanges)%in%GenomeInfoDb::seqlevels(refGRanges))) {
        GenomeInfoDb::seqlevels(inGRanges, pruning.mode = 'tidy') <- as.vector(newStyle)
      }
      
    }
  )
  
  return(inGRanges)
}