Question submitted via email:
I am using GENESIS R package to fit GLMM models to analyze genome-wide associations of SNPs with binary traits in a dataset with familial design. Running the "fitNullModel" and "assocTestSingle" functions (with family = "binomial" and test="Score") the results return Score/Score.SE for each SNP and, in addition, contain Est/Est.SE which are (according to user manual) approximations of effect sizes and their standard errors.
I appreciate if you can clarify if these Est/Est.SE approximations are based on a Wald's test? and if the family is kept as binomial or internally changed to gaussian to decrease the computational burden when Est/Est.SE are computed?
Also, is my understanding correct that when a GXE term is included, the effect sizes (Est.G, Est.G:env) are based on a Wald’s test and a binomial family?