[BioC] retrieving LD between two known SNPs with rsID

[Valerie Obenchain]

You could use the ensemblVEP package with a plugin.

LD plugin here:
http://www.ensembl.info/ecode/category/vep-plugins/


Valerie


On 01/14/2014 06:58 AM, Francesco Lescai wrote:
> Hi guys,
> this question might have come up already, but couldn’t find a quick solution to it.
>
> while there are several packages/functions available in Bioconductor to calculate pairwise LD from genetic datasets, if I have only two rs IDs of two SNPs, and want to know if they’re in LD, is there a way to download this value from some database?
> ENSEMBL does it on the fly, and therefore doesn’t seem to be available through biomart.
>
> thanks for the hints,
> Francesco
>
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-- 
Valerie Obenchain

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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