[BioC] Get all 3'utr and 5'utr region from GenomicFeatures

[Fabrice Tourre]

Steve,

It make sense.

Thank you very much.

On Tue, May 24, 2011 at 5:19 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Tue, May 24, 2011 at 9:18 AM, James W. MacDonald
> <jmacdon at med.umich.edu> wrote:
>> Hi Fabrice,
>>
>> On 5/24/2011 4:56 AM, Fabrice Tourre wrote:
>>>
>>> Dear list,
>>>
>>> How can I get all 3'utr and 5'utr region from GenomicFeatures of Human?
>>> There are fiveUTRsByTranscript, threeUTRsByTranscript methods in
>>> GenomicFeatures. But how can I get these regions?
>>
>> hg19 <- makeFeatureDbFromUCSC(genome = "hg19", table = "refGene")
>> utr3 <- threeUTRsByTranscript(ref19)
>>
>> Which seems pretty obvious to me, given the help pages for these functions.
>>
>> It would be helpful if you could give us an indication of where you got
>> stuck, and what in particular you didn't understand from the help pages, so
>> we can improve our documentation.
>
> Perhaps the OP wanted to know how to get the sequences from those
> regions, given the results from those functions?
>
> If that's the case, I'd load up the BSgenome.Hsapiens.UCSC.hg19
> library, iterate over my results one chromosome at a time, and use a
> mix of the Views function over the unmasked chromosome (using ranges
> across the 3'utr across the chromosome as the second argument) ...
> you'll have to take care of seqs on the reverse strand.
>
> You could also look at the getSeq function.
>
> I'lll leave the actual writing of the code as an exercise to the
> reader since I think it's useful to know how Views work and you'll
> have to read up on the documentation a bit :-)
>
> -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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>