R/find.kataegis.R

In jjellis/GenomicVis: Genomic Visualisation Routines

#' @import parallel
#' @import GenomicRanges
#' @import S4Vectors
#' @import IRanges
#' @import GenomeInfoDb
find.kataegis <- function(x, min.snvs, max.mean.distance,
	ncpus = getOption('cl.cores', 1)) {
  chrs <- as.character(runValue(seqnames(x)))
  if (ncpus > 1) {
    cl <- makeCluster(ncpus)
    # clusterEvalQ(cl, { library('GenomicRanges') })
    clusterExport(cl, 'reduceWithin', envir = environment())
    unlist(GRangesList(tryCatch({
	    parSapplyLB(cl = cl, chrs, find.kataegis.helper, x, min.snvs, max.mean.distance)
    },
    finally = {
	    stopCluster(cl)
    })))
  } else {
    unlist(GRangesList(sapply(chrs, find.kataegis.helper, x, min.snvs, max.mean.distance)))
  }
}