search

UW-GAC / GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
https://bioconductor.org/packages/GENESIS
34 stars 13 forks source link

Fix bug with SPA p-values for glm models #85

Closed amstilp closed 2 years ago

amstilp commented 2 years ago

In SPA_pval, the fitted.values for glm models already have the expit applied, so taking the expit again causes incorrect association test statistics.

amstilp commented 2 years ago

I am still testing this, but pushed the branch and started a pull review for commenting.

amstilp commented 2 years ago

After running Score.SPA tests using one of my glm models with the new code, it looks much better - assoc test statistics have a much better QQ plot.