The Hardy-Weinberg principle and estimating allele frequencies
We'll pick up where we left on on Tuesday, and you'll get introduced to more about estimating allele frequencies than you ever thought possible. It isn't just p = k/N, where k is the number of alleles in your sample and N or is the sample size. Well, to be precise, that can be the formula, but there's a lot more hiding behind that simple formula than you probably imagine.
- Estimating allele frequencies with the EM algorithm
- Estimating allele frequencies in the ABO blood group system (Bayesian version)
- Recording of lecture Note: The display did not record. You will see only a green screen, but you should here my voice. Sorry about that.
If you'd like to install Stan and try the examples I demonstrated in class, here are links to the software and installation instructions and to the Stan code I used. WARNING: To install and use Stan you'll need to have a C++ compiler installed. It really isn't necessary to learn Stan unless you get deeply into Bayesian inference and encounter some very challlenging problems. I'll illustrate a gentler approach to Bayesian inference later in the course
- Stan interfaces: For what it's worth, I'm most familiar with RStan. The Stanlanguage is the same regardless of which interface you use.
- R source for binomial analysis
- Stan source for binomial analysis
- R source for ABO analysis
- Stan source for ABO analysis