Hi, there:
I am amzed that the example code shared on this Github repository basically has only one line after merging the BETAs and SEs: hyprcoloc(betas, ses, trait.names=traits, snp.id=rsid)
Below is the output that I got from running this example code.
It seems to tell me that the first 5 traits co-localize at SNP rs11591147, and the next 3 trais co-localize at SNP rs12117612, correct? If so, this seems to test pleiotropy instead of colocalization, that is, one SNP is associated with multiple traits.
I genetarated P-values by using pvals = 2(1- pnorm(abs(betas/ses)))*. For the second co-localization SNP rs12117612, the last trait T10 also has a very significant P-value (1.76e-10). So, why T10 is not included in the second cluster?
Thank you & best regards,
Jie
Hi, there:
I am amzed that the example code shared on this Github repository basically has only one line after merging the BETAs and SEs: hyprcoloc(betas, ses, trait.names=traits, snp.id=rsid)
Below is the output that I got from running this example code.
It seems to tell me that the first 5 traits co-localize at SNP rs11591147, and the next 3 trais co-localize at SNP rs12117612, correct? If so, this seems to test pleiotropy instead of colocalization, that is, one SNP is associated with multiple traits.
I genetarated P-values by using pvals = 2(1- pnorm(abs(betas/ses)))*. For the second co-localization SNP rs12117612, the last trait T10 also has a very significant P-value (1.76e-10). So, why T10 is not included in the second cluster?
Thank you & best regards,
Jie