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dcgerard / ldsep

Linkage Disequilibrium Shrinkage Estimation for Polyploids
https://dcgerard.github.io/ldsep/
GNU General Public License v3.0
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LD pruning for PCA #6

Closed Homap closed 2 years ago

Homap commented 2 years ago

Dear David,

Thank you very much for your great R package. I have a question regarding LD pruning. I'd like to use the glpca function in adegenet package to conduct PCA in my samples (20 diploids individuals, 6 tetraploids and 4 hexaploids). I have pruned the SNPs for my diploid samples using plink, however, I am not sure how I could do that for my polyploids since plink does not accept polyploid data as input. When using ldsep and obtaining the matrix of pairwise LD, I was wondering how I could use that to prune my data for LD?

Thank you very much in advance, Homa

dcgerard commented 2 years ago

Hey Homa,

Thanks for your interest in {ldsep}!

Right now, I haven't implemented any LD pruning methods, but this is something that I plan on eventually getting to. I'll let you know when I get around to it.

Best, David

Homap commented 2 years ago

Thanks a lot, I am looking forward to it!