Why is the PP.H4.abf result of res$summary different from the maximum PP.H4 in res$results?

Question

Why is the PP.H4.abf result of res$summary different from the maximum PP.H4 in res$results?

dqq0404 opened this issue 5 months ago · 3 comments

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?

Answer 1 · 2024-04-12T06:14:51.000Z

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

…

-- https://chr1swallace.github.io

________________________________ From: dqq0404 ***@***.***> Sent: Friday, April 12, 2024 7:08:23 AM To: chr1swallace/coloc ***@***.***> Cc: Subscribed ***@***.***> 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? — Reply to this email directly, view it on GitHub<#161>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAQWR2EMAFL2NICVF7BGEE3Y4525PAVCNFSM6AAAAABGDRAY3KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTSMJVG44TQMI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

Answer 2 · 2024-04-12T06:58:15.000Z

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

Answer 3 · 2024-06-07T08:22:51.000Z

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?