Question: Linkage disequilibrium with 1000 Genomes/HapMap
2
gravatar for enricoferrero
5.4 years ago by
enricoferrero780
United Kingdom
enricoferrero780 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

ADD COMMENTlink modified 5.4 years ago by Mo Sander50 • written 5.4 years ago by enricoferrero780
0
gravatar for Mo Sander
5.4 years ago by
Mo Sander50
United Kingdom
Mo Sander50 wrote:

I think you should be able to use the package PLINK/SEQ for that, see also https://atgu.mgh.harvard.edu/plinkseq/tutorial.shtml

Sorry, I just saw that the R package is not available at the moment https://atgu.mgh.harvard.edu/plinkseq/download.shtml ...

 

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Mo Sander50
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