One of the reasons that I don’t post AdmixTools results too much is that the framework requires more statistical “deep thought” than just popping out a PCA or even running some model-based clustering. Read the methods supplements of one of the Reich lab’s papers, and you’ll see what I’m getting at. But a more prosaic reason is that I generally work in the plink format, and format conversion, as well as editing parameter files, is a pain. In general, I don’t do much “exploratory AdmixTools” stuff for a reason.
Martin Petr has made the second excuse a lot less of an excuse. His admixr package gives one an easy interface into AdmixTools. In particular, it allows one not to have to edit parameter files so much. It took me about ~15 minutes to get it downloaded and running. I’m on a Mac and for R use RStudio.
– remember to install wget if you are on a Mac (this will show up if you want to use online datasets)
– You need to make sure to set the path to AdmixTools. In the RStudio console, I just entered:
Sys.setenv("PATH"="~/MyPath/To/AdmixTools/bin/")
If you can get AdmixTools installed in the first place, admixr should be very easy.