[BioC] R packages for position anotation?

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Dec 14 20:28:22 CET 2010


On Tue, Dec 14, 2010 at 1:37 PM, Jinyan Huang <jhuang.ceph at gmail.com> wrote:
> Hi Steve,
> Thanks for your suggestion.
> What I understand your suggestion is I shoud use exonsBy,
> intronsByTranscript, fiveUTRsByTranscrip, threeUTRsByTranscript
> separately. For example, if I want to check whether a position is in
> exon or not. I do as fellow. But this is just suitable for one
> position each time. Is it possible to check many positions at the same
> time? Thanks.

I'm not sure which direction of "many" you are looking for. If you
want to test if multiple positions are in any exon, you can make your
`gr` GRanges object bigger (include those positions), and tease apart
your findOverlaps results by which subjectHits are overlapping with
which queryHits ...

Is that what you're asking?

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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