[BioC] retrieving LD between two known SNPs with rsID

Valerie Obenchain vobencha at fhcrc.org
Tue Jan 14 20:21:58 CET 2014

You could use the ensemblVEP package with a plugin.

LD plugin here:


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
> 	[[alternative HTML version deleted]]
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Valerie Obenchain

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: vobencha at fhcrc.org
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