[BioC] pintersect GRanges with empty results
Michael Lawrence
michafla at gene.com
Fri Aug 22 13:06:36 CEST 2014
Why not just use pintersect(exons, cds, resolve.empty="start.x")? Then drop
empty ranges from the result.
Michael
On Fri, Aug 22, 2014 at 3:12 AM, Christian Ruckert <cruckert at uni-muenster.de
> wrote:
> Hi all,
>
> I am searching a solution for the following problem:
>
> I have two GRanges objects, one with exon coordinates e.g.
>
> chr1 400 600 gene1 exon1
> chr1 800 900 gene1 exon2
> chr7 100 200 gene2 exon1
> chr7 300 500 gene2 exon2
>
> and one with the corresponding coding sequences coordinates.
>
> chr1 500 850
> chr1 500 850
> chr7 300 500
> chr7 300 500
>
> Coding regions were repeated accordingly, so that both GRanges have the
> same length.
>
> I want to restrict the exon GRanges object to the coding regions.
> pintersect looks promising but has problems if the two ranges don't overlap
> at all, which can happen if an exon falls completely within one of the UTRs
> (line 3 above). I tried to filter out these exons beforehand, but there is
> no parallel version of countOverlaps and I don't want to overlap the
> entries of the first GRanges with any of the second as there maybe
> different genes/transcripts at the same location.
>
> There must be a better solution than a for loop ;-)
>
> Regards,
> Christian
>
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