[BioC] R packages for position anotation?

[Jinyan Huang]

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.

>txdb <- loadFeatures(samplefile)
>annotGr <- exonsBy(txdb, "tx")
>gr <- GRanges( seqnames = c("chr11"),
 ranges = IRanges(start = c(74994500),
 end = c(74994500)),
 strand = c("-"))
>OL <- findOverlaps(query = annotGr, subject = gr)
>tdata <- annotGr[unique(queryHits(OL)),]
>tdata
GRangesList of length 2
$44081
GRanges with 16 ranges and 3 elementMetadata values




On Mon, Dec 13, 2010 at 5:23 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> 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
>
> --
> 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
>