Thanks Valerie.

One more question if you don't mind. I am annotating several thousand SNPs.
The number of SNPs allocated to 3'UTR or 5'UTR are exactly the same. I will
have expected more from the 3'UTR as the 3'UTR is much longer than 5'UTR.
Is this a lucky coincidence? Sorry for the vagueness of the question.
Thanks.



On Thu, Apr 4, 2013 at 11:56 AM, Adaikalavan Ramasamy <
adaikalavan.ramasamy@gmail.com> wrote:

> Thanks. That will be a useful feature.
>
> In the meantime I will try to delete manually when intergenic snps are too
> far from the precede or follow ids. Thanks.
>
> Thanks. That will be a useful feature.
>
> In the meantime I will try to delete manually when intergenic snps are too
> far from the precede or follow ids. Thanks.
> Valerie Obenchain <vobencha@fhcrc.org> wrote:
> 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@fhcrc.org
> > <mailto:vobencha@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@r-project.org <mailto:Bioconductor@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@r-project.org <mailto:Bioconductor@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>
> >
> >
>
>
> 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@fhcrc.org
> > <mailto:vobencha@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@r-project.org <mailto:Bioconductor@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@r-project.org <mailto:Bioconductor@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>
> >
> >
>
>
>

	[[alternative HTML version deleted]]

