I was wondering how I could include a dominance effects matrix into a GWAS using Sommer. I’m not entire sure how the syntax would change or if I should use the GWAS() function or the mmer() funcition. I couln’t find a specific example for this so far online.

So if this is the funcition that I’m using:

`mix2 <- GWAS(R2~1,
         random=~vs(id,Gu=Aa),
         rcov=~units,
         data=phenorm,
         n.PC = 3,
         M= Xz, gTerm = "u:id")`

Would I need to simply add another term to the random terms that has the dominance matrix (from D.mat())? I’m guessing I also need to do some changes in M and gTerm but I’m not entirely sure what changes.