r2 and LD value estimation between significant SNPs identified from GWAS
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2.9 years ago
rthapa ▴ 50

Hi,

I want to estimate r2 value and LD value among the significant SNPs discovered from GWAS analysis. Could anyone suggest me what R package is the best and what file format is needed? I would appreciate it.

Thanks

SNP R • 1.7k views
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2.9 years ago
zx8754 11k

There are many packages that can do that, depends what format your data is.

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Thank you for your reply. Finally I could use TASSEL to get r2 value. I wanted to see LD decay using r2 and distance but my plot looks weird. Do you have any idea?

Thanks!

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