[Bioc-devel] rtracklayer: Export to bigwig with unused seqlevels

Thanks, should be resolved in 1.23.20 (devel).


On Fri, Mar 28, 2014 at 8:09 AM, Julian Gehring <julian.gehring at embl.de
<mailto:julian.gehring at embl.de>> wrote:

    Hi,

    Exporting a GRanges object to the 'bigwig' format with rtracklayer fails
    if not all seqlevels are used:

    #+BEGIN_SRC R
      library(rtracklayer)
      library(GenomicRanges)

      ## example data
      example(GRanges)
      lg = reduce(unstrand(longGR))
      lg$score = 1:6

      ## full one works
      export(lg, tempfile(), "bw") ## works

      ## generally works if all seqlevels are used
      lg1 = lg[c(1, 3, 5)]
      export(lg1, tempfile(), "bw") ## works

      ## subset works if all seqlevels are used
      lg2 = lg[1:4]
      export(lg2, tempfile(), "bw") ## fails

      lg3 = keepSeqlevels(lg2, unique(as.character(seqnames(lg2))))
      export(lg3, tempfile(), "bw") ## works
    #+END_SRC

    This fails with the latest bioc-devel (rtracklayer_1.23.18) and works
    with bioc-stable.

    A solution may be to remove unused seqlevels in the object, perhaps with
    a warning/message that not all seqlevels were exported.

    Best wishes
    Julian