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Published 20 hours ago • verified publisher icon zhengxwen

snpgdsLDpruning for getting the number of independent markers for GWAS

Open MuBulut opened this issue 3 years ago • 2 comments

Hi, I was using the snpgdsLDpruning function to determine the actual number of independent SNPs in my genotype file, to perform BF correction for my GWAS. The function gives me a number of marker, which are selected (see fig. 24802 Markers). My question: Is this the number of the independent Markers (BF = 0.05/24802), or is it the number of SNPs which are in LD (0.05/(3613062-24802))?

Thanks in advance. M. image

MuBulut avatar Jan 17 '22 14:01 MuBulut

It is the number of the approx. independent Markers.

zhengxwen avatar Feb 02 '22 09:02 zhengxwen

nice thanks this helps a lot, and btw is there a way how to define/calculate the right sliding windows for calculating the numbers of independent markers?

MuBulut avatar Feb 02 '22 09:02 MuBulut