Question: regioneR, but for Linkage Disequilibrium, not just overlap?
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gravatar for Philipp Bayer
11 months ago by
Philipp Bayer5.6k
Australia/Perth/UWA
Philipp Bayer5.6k wrote:

I've got two sets of candidate genes and my 'background' of all genes. I think the LD in those two sets differs somewhat from the other, but looking at LD triangle plots doesn't really cut if since there's always a bit of noise there. I can't just take the 'average' LD within those two sets of genes since there are many 0/1 LD SNPs.

regioneR is a nifty package which tests different candidate regions whether they're associated based on overlaps. Is there something like this, but which goes a bit further and checks whether LD is (significantly?) different between two sets of candidate genes? I wouldn't know how to implement that, for starters the SNP density, the SNP missingness, etc. pp. could be different...

snp ld • 504 views
ADD COMMENTlink written 11 months ago by Philipp Bayer5.6k
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