Analyzing the genetic structure of populations: individual assignment

Today we'll explore the logic behind STRUCTURE. As mentioned in the notes for this week's lab, I'd intended to use it for the lab exercise. We'll be using LEA instead. It fits the same basic model that STRUCTURE fits, but it uses a constrained least squares optimization to do so rather than a Bayesian approach. I haven't compared the two with real or simulated datasets, but the difference should be fairly small. The Frichot et al. paper linked below provides all of the gory details on LEA if you want to see them.

Online notes

Associated readings

Frichot, E., F. Mathieu, T. Trouillon, G. Bouchard and O. François. 2014. Fast and efficient estimation of individual ancestry coefficients. Genetics 196:973-983. link