Credible set is a set of SNPs with the lowest p-value

[PhoebeGuo97]

Hello, I run susie_rss for one interested locus with ~1000 SNPs. It converged and lambda was ~0.19. There is one CS with 15 SNPs in the output (see below) and these 15 SNPs are also the SNPs with the lowest p values in that region. I'm wondering if that's suspicious. Thanks!

rss$sets$cs $L1 [1] 497 515 538 540 889 898 903 919 923 925 928 932 976 978 981

[pcarbo]

@PhoebeGuo97 Quite the opposite, that sounds like the right result. Can you share the full rss$sets?

[PhoebeGuo97]

Hello @pcarbo, here is the full rss$sets:

$cs $cs$L1 [1] 497 515 538 540 889 898 903 919 923 925 928 932 976 978 981

$purity min.abs.corr mean.abs.corr median.abs.corr L1 0.7630299 0.8993411 0.955967

$cs_index [1] 1

$coverage [1] 0.9513883

$requested_coverage [1] 0.95

[pcarbo]

Those results look reasonable — I don't see any cause for concern.

[PhoebeGuo97]

Good to know. Thank you!