4 months ago by
Glasgow - UK
Some options that pop up to my mind:
Applied Statistical Genetics with R I don't know this book, but these "Use R!" books are generally pretty good.
The R Book I found it really good to get started with R. It's R with mostly examples from ecology and evolution. So may be not what you are looking for. (Google finds the full pdf of this book)
Bioconductor packages comes with vignettes that often are quite useful not just to understand the package but also to understand the theory behind (limma, edgeR, deseq are great, but it's not quantitative genetics). There are hundreds of packages so you will have to sieve through and see if there is something useful for you.