It has been a while, but I need to make sure that EMMA works for Dr. Kleeberger’s project

Understand the population genetics

A hands on tutorial here.

Understand the Mixed model

plink provides many good tools.

Implementation with R — I encountered some hurdles with R programming and would like to document them here before I forget.

If fctr.cols are the names of your factor columns, to convert
them to characters

X[, fctr.cols] <- sapply(X[, fctr.cols], as.character)

distances <- matrix(1:25, nrow=5, ncol=5)
Now, 
apply(distances, c(1, 2), function(x) 0)
distances[] <- 0L
distances*0

Viewing/reporting the results

I found a very useful and handy help doc on Manhattan Plot