[BioC] Linkage disequilibrium with 1000 Genomes/HapMap

[Valerie Obenchain]

Hi,

You might want look at the trio package.

http://www.bioconductor.org/packages/release/bioc/html/trio.html

getLD() and getLDlarge() compute LD values genome-wide; findLDblocks() 
plots the LD matrix and estimates LD blocks. The functions can be 
applied to non-trio data by using the 'parentsOnly' argument.

cc'ing the package author in case he has something else to add.

Valerie



On 07/21/2014 01:31 PM, Enrico Ferrero wrote:
> Hi,
>
> I have a set of SNPs associated with a specific trait and I would like
> to know to what other SNPs, in the 1000 Genomes [1] or HapMap [2]
> projects, they are in linkage disequilibrium (LD) with.
>
> Is there anything in Bioconductor (or CRAN) that can help me answer
> this question? I'm basically looking for something like SNAP Pairwise
> LD [3] from the Broad Institute.
>
> Thanks!
>
> [1] http://www.1000genomes.org/
> [2] http://hapmap.ncbi.nlm.nih.gov/
> [3] https://www.broadinstitute.org/mpg/snap/ldsearchpw.php
>


-- 
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fhcrc.org
Phone: (206) 667-3158