Why is the PP.H4.abf result of res$summary different from the maximum PP.H4 in res$results?
dqq0404 opened this issue · 5 comments
dqq0404 commented
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
PP.H4 is explained here https://chr1swallace.github.io/coloc/articles/a03_enumeration.html does that help?
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Subject: [chr1swallace/coloc] Why is the PP.H4.abf result of res$summary different from the maximum PP.H4 in res$results? (Issue #161)
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
Thanks!! I probably understand, so this result is correct.
dqq0404 commented
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?