[BioC] R packages for position anotation?

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Dec 13 17:23:04 CET 2010


On Mon, Dec 13, 2010 at 10:59 AM, Jinyan Huang <jhuang.ceph at gmail.com> wrote:
> Dear all,
> Is there a Bioconductor packages can do like something like this?
> Giving a position, it can tell where this position locate in the gene
> (3' UTR, 5' UTR Exon, intron and so on).

With a bit of coding, you can use the GenomicFeatures package to get this info.

Build your TranscriptDb, then look at the help pages in ?transcriptsBy

If you store your query positions in a GRanges object, you can use the
results returned from the functions above with
findOverlaps/countOverlaps to find your hits.


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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