R/dropDictyChromosomes.R

In WilliamSalvidge/dictyChipSeq: What the Package Does (One Line, Title Case)

#' dropDictyChromsomes
#'
#' Function to drop any chromsomes which are not d. discoideum chromsomes 1 through 6
#' Extra chromosomes and contigs - ribosomal, mitochondrial etc. may be interesinting but this
#' is just for simplicity
#'
#' @param x Granges object
#'
#' @return Granges object
#' @export
dropDictyChromosomes = function(x) {

  dictyChromosomes1to6 = c("DDB0232428", "DDB0232429", "DDB0232430",
                           "DDB0232431", "DDB0232432", "DDB0232433")


  return (GenomeInfoDb::dropSeqlevels(x,
                                      GenomeInfoDb::seqlevels(x)[ ! ( GenomeInfoDb::seqlevels(x) %in% dictyChromosomes1to6)],
                                      pruning.mode=c("coarse")))

}