[BioC] definition for intergenic SNPs in locateVariants function

[Valerie Obenchain]

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
>
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