Martin Lysy, Peter W.J. Kim, Terin Robinson
Tools for the analysis of population differences using the Major Histocompatibility Complex (MHC) genotypes of samples having a variable number of alleles (1-4) recorded for each individual. A hierarchical Dirichlet-Multinomial model on the genotype counts is used to pool small samples from multiple populations for pairwise tests of equality. Bayesian inference is implemented via the rstan package. Bootstrapped and posterior p-values are provided for chi-squared and likelihood ratio tests of equal genotype probabilities.
To install the latest R release:
install.packages("MADPop")
To install the latest development version, first install the R package devtools then run
devtools::install_github("mlysy/MADPop")
Please see tutorial here or by running vignette("MADPop-quicktut").
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