R/exportTracks.R

In Ringo: R Investigation of ChIP-chip Oligoarrays

exportCherList <- function(object, filename="chers.gff", format="gff3", genome="hg18", ...)
{
  require("rtracklayer")
  stopifnot(inherits(object, "cherList"))
  chersDf <- as.data.frame.cherList(object)
  chersDf$strand <- NA
  chersDf$chrom <- paste("chr", sub("^chr", "", chersDf$chr), sep = "")
  chersDf$start <- as.integer(as.character(chersDf$start))
  chersDf$end <- as.integer(as.character(chersDf$end))
  cherRanges <- IRanges(chersDf$start, chersDf$end)
  cherTrack  <- GenomicData(cherRanges,
                            chersDf[, c("strand", "name", "antibody")],
                            chrom = chersDf$chrom,
                            genome = genome)
  ## old stuff, does not work with rtracklayer >= 1.7.0
  #chersAdf <- as(chersDf, "AnnotatedDataFrame")
  #descs <- c(chrom = "Chromosome ID",
  #           start = "Start position on chromosome",
  #           end = "End position on chromosome",
  #           strand = "DNA strand, sense (+) or antisense (-)")
  #md <- data.frame(labelDescription = descs, stringsAsFactors = FALSE)
  #varMetadata(chersAdf)[rownames(md),] <- md
  #cherTrack <- rtracklayer:::trackSet(chersAdf, ...)
  export(cherTrack, filename, format=format)
  invisible(NULL)
}# exportCherList