[BioC] definition for intergenic SNPs in locateVariants function

[Valerie Obenchain]

On 04/03/13 17:10, Adaikalavan Ramasamy wrote:
> Dear Valerie,
>
> Do you mean there is no limit on the flanking gene? Even if it is say
> 10Mb away?

Yes, that's correct.

Since upstream/downstream distance is relevant for eQTL analysis it 
sounds like this functionality would be useful for a wider audience. 
I've put this on my TODO for the next devel cycle. Thanks for the 
suggestion.

Valerie
>
> I am working on eQTLs where most people assume the cis-eQTLs operate on
> a gene located a short distance away (< 1Mb) so we may want to treat
> those that are located very far away differently. Thanks.
>
> Regards, Adai
>
>
>
>
> On Wed, Apr 3, 2013 at 4:33 PM, Valerie Obenchain <vobencha at fhcrc.org
> <mailto:vobencha at fhcrc.org>> wrote:
>
>     Hi Adai,
>
>     The intergenic SNPs are those that fall outside of the gene ranges
>     defined in the annotation. There is a table in the vignette that
>     briefly describes this.
>
>     With a txdb as the annotation, "transcripts by gene" are extracted
>     and findOverlaps() is performed with the variant ranges. Variants
>     that do not have a 'hit' are considered to fall outside gene
>     regions. For these variants we determine which genes fall to either
>     side (PREDEDEID and FOLLOWID in the output). There is no limit for
>     upstream/downstream searching. We simply take the next closest gene
>     if one exists.
>
>     If you were able to define upsteam/downstream limits I'm assuming
>     you're interested in all genes that fell in that range, not just the
>     next closest gene?
>
>     Valerie
>
>
>
>
>     On 04/03/2013 05:31 AM, Adaikalavan Ramasamy wrote:
>
>         Dear all,
>
>         I have been using the locateVariants function in the
>         VariantAnnotation
>         package. It has been great and we are now in the process of
>         writing the
>         methods section.
>
>         May I know how the intergenic SNPs were defined? What is the
>         limit upstream
>         and downstream to define PRECEDEID and FOLLOWID. I check the
>         manuals and
>         mailing list without much luck.
>
>         This is of less importance but is there a way to adjust these
>         definition/limit if we want to do so in future? Thank you.
>
>         Regards, Adai
>
>                  [[alternative HTML version deleted]]
>
>         _________________________________________________
>         Bioconductor mailing list
>         Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>         https://stat.ethz.ch/mailman/__listinfo/bioconductor
>         <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>         Search the archives:
>         http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>         <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>
>
>     _________________________________________________
>     Bioconductor mailing list
>     Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>     https://stat.ethz.ch/mailman/__listinfo/bioconductor
>     <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>     Search the archives:
>     http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>
>