LD-correction for non-HapMap3 snps
Closed this issue · 1 comments
amc-corey-cox commented
Using LD-correction in the HOPS software appears to prune the data-set to HapMap3 snps, all others have P_scores of NA. Can you share how to calculate the LD correction metric you use so that I can try to calculate this for other snps in my data-set? I have a fair number of snps with low p-values from a METAL analysis of 4 data-sets that end up with NA P_scores when LD-corrected is set to TRUE.
Can we have an options to provide our own LDscores data with some guidance on how to calculate it?
amc-corey-cox commented
Looks like this is orphaned and I want it off my issues page.