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chr1swallace / coloc

Repo for the R package coloc
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Why is the PP.H4.abf result of res$summary different from the maximum PP.H4 in res$results? #161

Open dqq0404 opened 2 months ago

dqq0404 commented 2 months ago

Hi, The res$summary results I get are as follows: nsnps PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf 2.863000e+03 4.089385e-20 6.817232e-18 2.355242e-04 3.830173e-02 9.614627e-01 But when I opened res$results, I found that the largest PP.H4 was only 1.808670e-01. What's the problem?

chr1swallace commented 2 months ago

PP.H4 is explained here https://chr1swallace.github.io/coloc/articles/a03_enumeration.html does that help?

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Hi, The res$summary results I get are as follows: nsnps PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf 2.863000e+03 4.089385e-20 6.817232e-18 2.355242e-04 3.830173e-02 9.614627e-01 But when I opened res$results, I found that the largest PP.H4 was only 1.808670e-01. What's the problem?

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dqq0404 commented 2 months ago

Thanks!! I probably understand, so this result is correct.

dqq0404 commented 1 month ago

Hi, my PP.H4.abf is 0.877, and the max SNP.PP.H4 is 0.19. Can I use this SNP as the causal SNP?