How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice
This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid certain SNPs being removed during 'clumping'.. And second, if the SNP of interest is removed during clumping, is there a way to find out which SNP in LD is included (instead of the one I am interested in) in the PRS calculation?
1 answer
- You can "retain" a SNP of interest by manually setting their p-value at 0 (though that will also mean that you won't really be able to do p-value threshold)
- If you want to check that, the best way is to "dry" run PRSice once with
--no-clump --print-snpoption, which will generate a .snp file. You can then clump your data set using PLINK with the--extract PRSice.snpoption to obtain the information you wanted.
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