Repository files navigation

Martin Lysy, Peter W.J. Kim, Terin Robinson

Tools for the analysis of population differencesusing the Major Histocompatibility Complex (MHC) genotypes of sampleshaving a variable number of alleles (1-4) recorded for eachindividual. A hierarchical Dirichlet-Multinomial model on thegenotype counts is used to pool small samples from multiplepopulations for pairwise tests of equality. Bayesian inference isimplemented via therstan package. Bootstrapped and posteriorp-values are provided for chi-squared and likelihood ratio tests ofequal genotype probabilities.

To install the latest R release:

install.packages("MADPop")

To install the latest development version, first install the R packagedevtools then run

devtools::install_github("mlysy/MADPop")

Please see tutorialhere or by runningvignette("MADPop-quicktut").