Following this, I then run susie.resA <- coloc.susie(D1_coloc_susie, D2_coloc_susie), and I would expect there to be 6 rows in the summary susie.resA$summary (with each row summarizing the possible pairwise comparisons between the 2 credible sets from D1 and the 3 credible sets from D2 ). However, there are only 2 rows in the summary:
Might you be able to help me understand why there are only two comparisons in susie.resA$summary rather than 6 as I would expect?
I am also perplexed by the 2nd credible set from D1 (colored in green)... does it make sense that these SNPs are identified as a "credible set" even though they all have -log10(pval) close to 0 in the Manhattan plot?
Hi Chris,
I hope this message finds you well. I am trying to run coloc.susie() for two datsets D1 and D2 and am having some trouble:
D1_coloc_susie <- runsusie(D1)
returns 2 credible sets insummary(D1_coloc_susie)
:D2_coloc_susie <- runsusie(D2)
returns 3 credible sets insummary(D2_coloc_susie)
:susie.resA <- coloc.susie(D1_coloc_susie, D2_coloc_susie)
, and I would expect there to be 6 rows in the summarysusie.resA$summary
(with each row summarizing the possible pairwise comparisons between the 2 credible sets from D1 and the 3 credible sets from D2 ). However, there are only 2 rows in the summary:susie.resA$summary
rather than 6 as I would expect?I am also perplexed by the 2nd credible set from D1 (colored in green)... does it make sense that these SNPs are identified as a "credible set" even though they all have -log10(pval) close to 0 in the Manhattan plot?
Thank you in advance, Chris A