chr1swallace/coloc

Interpretation on SNP.PP.H4

zl2860 opened this issue · 2 comments

zl2860 commented

Hello, I am new to this amazing R package and just got confused about some outputs from the function coloc.abf().

I know that PP.H4 is the posterior probability of sharing the causal variant, but when PP. H4 is > 95%, how should I interpret the individual SNP.PP.H4 when its value is 0.01? I

I saw on the tutorial that individual SNPs with SNP.PP.H4 > 0.01 were selected as more likely to be the shared causal variants. How should I understand or interpret the value 0.01, when putting the PP.H4>0.95 and the SNP.PP.H4=0.01 together? Does it mean that given H4 is >95% true, the probability of the individual SNP to be the shared causal variant is 0.01? is this value (0.01) too low for further exploration?

Thanks!

chr1swallace commented
zl2860 commented

Thanks for your reply! Now I have one more question about defining the shared causal variant. Say if H4 is true, then is there any recommended cut-off value for SNP.PP.H4 to define the shared causal variant? In the tutorial, it seems that 0.01 acts as such a cut-off value, but is it too low or it is treated as ana acceptable threshold in genetic studies?