p-value for the interaction term between G*E

[hmtsao]

Hi,

In the TrajGWAS documentation (https://openmendel.github.io/TrajGWAS.jl/dev/#GxE-or-other-interactions), the p-value file from jointly testing for G + G*E using the formula testformula=@formula(y ~ snp + snp & sex) includes betapval, taupval, and jointpval.

Is the betapval for the snp? How can I obtain the beta coefficient and betapval for the interaction term (snp*sex)?

Thanks!

[kose-y]

Betapval is the p-value for

null hypothesis: both G and GE effect sizes are zero;
alternative hypothesis: either effect size for G or GE is nonzero.

The default test type in this package is the score test, which only computes p-values, not the exact values of effect sizes, for efficiency. If you need the effect sizes directly, please pass the keyword argument test=:wald to the trajgwas function.