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chr1swallace / coloc

Repo for the R package coloc
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Interpretation on SNP.PP.H4 #112

Open zl2860 opened 1 year ago

zl2860 commented 1 year ago

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 1 year ago

Does it mean that given H4 is >95% true, the probability of the individual SNP to be the shared causal variant is 0.01? Yes, almost exactly. If​ H4 is true (it can't be 95% true, it is either true or false, and PP.H4=95% suggests there is a 95% chance it is true), then this snp has an 0.01 chance to be the shared causal variant.

-- https://chr1swallace.github.io

From: zl2860 @.> Sent: 13 January 2023 08:46 To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] Interpretation on SNP.PP.H4 (Issue #112)

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!

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zl2860 commented 1 year ago

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?