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

[Julian Gehring]

Hi Michael,

Thanks, works all fine now.

Best wishes
Julian


On 28/03/14 22:05, Michael Lawrence wrote:
> 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
> 
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>