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