Summary from coloc.susie is missing pairwise comparisons between credible sets?

[char4816]

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 in summary(D1_coloc_susie):

 cs cs_log10bf cs_avg_r2 cs_min_r2
  1  17.880854 1.0000000 1.0000000
  2   3.762071 0.9853572 0.8502394

• D2_coloc_susie <- runsusie(D2) returns 3 credible sets in summary(D2_coloc_susie):

 cs cs_log10bf cs_avg_r2 cs_min_r2
  2   5.398681 1.0000000 1.0000000
  1  75.464148 0.9919625 0.9919625
  3   4.104218 0.7033808 0.2909467

• 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:

   nsnps            hit1            hit2    PP.H0.abf    PP.H1.abf    PP.H2.abf PP.H3.abf    PP.H4.abf idx1 idx2
1:   380 17:39895095:G:A 17:39899863:T:C 1.170962e-91 6.078599e-75 1.926368e-17 0.9999998 1.627483e-07    1    1
2:   380 17:39795779:A:G 17:39899863:T:C 1.638628e-77 6.061780e-75 2.695732e-03 0.9972328 7.145764e-05    2    1

1. 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?
2. 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