R/hic_export.R

In ComunidadBioInfo/HiConvert: What the Package Does (One Line, Title Case)

#' Exports HiC file
#'
#' Exports an GAlignment object to a file with the specified format
#'
#' @param x A GAlignmentPairs object
#' @param file path or name of the output file
#' @param format the file format to export
#'
#' @return A sequence file with the specified format
#' @importFrom GenomicRanges granges seqnames start end
#' @export
#'
#' @examples
#' x <- hic_import("example.bam")
#' hic_export(x, "example.bedpe", format = "bedpe")
#' hic_export(x, "example.bam", format = "bam")

hic_export <- function(x, file, format) {
  gfirst <- granges(x@first)
  gsecond <- granges(x@last)
  if (format == "bedpe") {
    output_bedpe <- data.frame(chrom1 = seqnames(gfirst),
                               start1 = start(gfirst),
                               end1 = end(gfirst),
                               chrom2 = seqnames(gsecond),
                               start2 = start(gsecond),
                               end2 = end(gsecond),
                               name = names(x) ,
                               score = ".",
                               strand1 = strand(gfirst),
                               strand2 = strand(gsecond),
                               others = ".")
    write.table(output_bedpe, file = file, row.names = FALSE,
	    col.names = FALSE, quote=FALSE, sep="\t")
   }
  if (format == "bam") {
    export(x, file, format = format)
  }
}