Controls / cases counts inverted when using binary model about staarpipeline-tutorial HOT 2 OPEN

Hi @GACGAMA,

Since you are working on variant-set analysis, is your Cases_Sum_nHet defined as the sum of heterozygous calls across all case samples, or is it the total number of heterozygous carriers among case samples?

Overall, this is possible, as the effect sizes of different variants in the variant set could be in various directions- some variants have a protective effect, while others may have a deleterious impact on the outcome. As such, the heterozygous counts may not always be enriched in the case samples.

from staarpipeline-tutorial.

Hi @xihaoli
In this case, the Cases_Sum_nHet is defined as the sum of the heterozygous carriers among case samples for each specific gene-function pair, such as gene-plof for example.
Is there any better way to find the direction of enrichment for each category of enriched genes?

from staarpipeline-tutorial.