Hi,
Many thanks for developing this package, it has been very useful for me that it relaxes the single causal variant assumption in the Coloc method.
My question is can you or how to extract the predicted causal SNP after I run pwcoco. In the coloc package, one is able to go into the results dataframe and extract the predicted causal SNP by using for example:subset(my.res$results,SNP.PP.H4>0.80) or by credible sets, for example:
o <- order(my.res$results$SNP.PP.H4,decreasing=TRUE)
cs <- cumsum(my.res$results$SNP.PP.H4[o])
w <- which(cs > 0.95)[1]
my.res$results[o,][1:w,]$snp
Hi, Many thanks for developing this package, it has been very useful for me that it relaxes the single causal variant assumption in the Coloc method.
My question is can you or how to extract the predicted causal SNP after I run pwcoco. In the coloc package, one is able to go into the results dataframe and extract the predicted causal SNP by using for example:subset(my.res$results,SNP.PP.H4>0.80) or by credible sets, for example: o <- order(my.res$results$SNP.PP.H4,decreasing=TRUE) cs <- cumsum(my.res$results$SNP.PP.H4[o]) w <- which(cs > 0.95)[1] my.res$results[o,][1:w,]$snp
Can I do the same for pwcoco results?
Many thanks Kindest Regards Xiyun