Entering edit mode
2.1 years ago
Mahan
▴
70
I'm working on PRS construction using lassosum package.
Once I obtain the best lambda value from the validation step, how can I see the final number of SNPs used in best.pgs in the following step?
out2 <- subset(out, s=v$best.s, lambda=v$best.lambda)
v2 <- validate(out2, covar=covar, test.bfile="Some_new_bfile")
My understanding is that we start with a certain number of SNPs from the summary stat based on p value cut off and then we select the SNPs with non-zero estimates.
TIA
