In a recently published Bioconductor vignette of apeglm: https://bioconductor.org/packages/devel/bioc/vignettes/apeglm/inst/doc/apeglm.html#Modelingratiosof_counts,
it detail a method of modelling allelic imbalance or ASE using a model however I have some question about the steps to complexify the base model. Essentially, I have 4 hybrid individuals, with 2 counts (2 species), in 3 conditions within a continuum. I would like to test the following design ~condition + species + condition:species.
I imagine within the first step : The model matrix would be shifted to x<- model.matrix(~Condition + species + Condition:species)
and the coef would of course be ajusted to to column within this model which we want to test.
The point which I have the most trouble is when testing the interaction: As the threshold argument would not necessarily be 0.5 ?
fit2 <- apeglm(Y=ase.cts, x=x, log.lik=NULL, param=param, coef=coef, mle=mle, threshold=0.5, log.link=FALSE, method="betabinCR")
Is there a way through apeglm to test this interaction ?