Hello,

Can the apeglm software be used to model (and test) the allelic imbalance (AI) as well as its shift between conditions? In the F1000 article, it is stipulated that estimating the intercept "in an intercept only model' is equivalent to the overall Allelic imbalance, which would suggest in a normal scenario using all sample of a similar nature. What I am wondering more specifically, is to assess the AI overall as well using samples with different condition, would the intercept remain an equivalent approximation of the basic allelic imbalance? If not, could one proceed to get this information using all sample (for a better model) as well as the in between condition shift using apeglm? Thank you !

You could use a model matrix with contrast coding, eg an intercept and then -1/2 and 1/2 to specify differences between two groups for example. Then the intercept will still correspond to the overall allelic ratio.