It took me a bit longer to make sure the data and associated scripts were performing the way I wanted them to, but the lab exercise for week 13 is now posted. You’ll be running a genome-wide association analysis on a subset of data collected in an analysis of gypsy moths (Lymantria dispar). This is only an example. You can look at the Stan code if you want. If you do, you’ll see that it’s just the linear regression that we’ll discuss in class on Thursday with some magic added to take care of the relatedness among individuals. If you were doing a real GWAS, I wouldn’t recommend using this script. I’d recommend using GEMMA or something like it that was built by experts in GWAS specifically for the purpose of GWAS. There are a lot of things to be careful about that aren’t built into these simple scripts, but they illustrate the principle so that you can get a sense of how GWAS might be used in your own research.
As usual, you can find a link to the lab from the Lecture Schedule page (or you can in a few minutes when I get it posted) or from the link here.