MADPop: 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.

Version: 1.1
Depends: R (≥ 3.0.2), rstan (≥ 2.14.1)
Imports: stats, utils, Rcpp (≥ 0.12.9), methods (≥ 3.3.2)
LinkingTo: StanHeaders (≥ 2.14.0.1), rstan (≥ 2.14.1), BH (≥ 1.62.0.1), Rcpp (≥ 0.12.9), RcppEigen (≥ 0.3.2.9.0)
Suggests: knitr, rmarkdown
Published: 2017-01-18
Author: Martin Lysy [cre, aut], Peter W.J. Kim [aut], Terin Robinson [ctb]
Maintainer: Martin Lysy <mlysy at uwaterloo.ca>
License: GPL-3
NeedsCompilation: yes
CRAN checks: MADPop results

Downloads:

Reference manual: MADPop.pdf
Vignettes: Bayesian Testing of Equal Genotype Proportions between Multiple Populations
Package source: MADPop_1.1.tar.gz
Windows binaries: r-devel: MADPop_1.1.zip, r-release: MADPop_1.1.zip, r-oldrel: not available
OS X Mavericks binaries: r-release: MADPop_1.1.tgz, r-oldrel: not available

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