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]]

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 > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Valerie Obenchain Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B155 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: vobencha at fhcrc.org Phone: (206) 667-3158 Fax: (206) 667-1319