MHC Allele-Based Differencing Between Populations

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.


Reference manual

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1.1 by Martin Lysy, a month ago

Browse source code at

Authors: Martin Lysy [cre, aut], Peter W.J. Kim [aut], Terin Robinson [ctb]

Documentation:   PDF Manual  

GPL-3 license

Imports stats, utils, Rcpp, methods

Depends on rstan

Suggests knitr, rmarkdown

Linking to StanHeaders, rstan, BH, Rcpp, RcppEigen

See at CRAN