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stephenslab / susieR

R package for "sum of single effects" regression.
https://stephenslab.github.io/susieR
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High PIP but not in credible sets #144

Closed katherinef closed 2 years ago

katherinef commented 2 years ago

Hello,

I have run susie_rss for a large region and obtain two credible sets. When I plot the PIPs I notice there are a number of variants with high PIPs but that are not in either credible set (see attached). I looks to me like there should be a third credible set. Do you have any suggestions for what I might try?

Many thanks,

Kath susieplot

gaow commented 2 years ago

@katherinef I assume you are referring to the variables around position 7000. In order for variables to be in a rho credible set, their PIP have to sum to greater than or equal to rho, and their "purity", defined by minimum absolute pairwise correlation, should be greater than or equal to r. Currently, rho is set to 0.95 and r is set to 0.5. You can lower either these numbers, or both, to be more lenient with credible sets, depending on your analysis context (current default is what we believe reasonable for genetic fine-mapping applications)

katherinef commented 2 years ago

Thank you very much - that's really helpful.