chr1swallace
commented
2 years ago H1, h2, use finemap.abf. hp doesn't correspond to any individual snp. If you believe h3 is true, then I would use the per trait per snp results from finemap.abf to infer the most likely causal variants for each.
https://chr1swallace.github.io
From: zillurbmb51 @.> Sent: Sunday, May 8, 2022 3:29:59 PM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] How to find H0 to H3 from the coloc.abf output for each snp (Issue #85)
Hi, The coloc.abf gives us summary (PP for H0-4) and dataframe with the following columns: "snp" "position" "V.df1" "z.df1" "r.df1" "lABF.df1" "V.df2" "z.df2" "r.df2" "lABF.df2" "internal.sum.lABF" "SNP.PP.H4"
How could we find the PP for other hypothesis (H0-3) for each snp?
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Hi, The coloc.abf gives us summary (PP for H0-4) and dataframe with the following columns:
"snp" "position" "V.df1" "z.df1" "r.df1" "lABF.df1" "V.df2" "z.df2" "r.df2" "lABF.df2" "internal.sum.lABF" "SNP.PP.H4"How could we find the PP for other hypothesis (H0-3) for each snp?