Interpretation on SNP.PP.H4
zl2860 opened this issue · 2 comments
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!
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?