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:	1.1.7
Depends:	R (≥ 3.4.0), rstan (≥ 2.26.0)
Imports:	methods, Rcpp (≥ 0.12.0), stats, rstantools
LinkingTo:	BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), rstan (≥ 2.26.0), StanHeaders (≥ 2.26.0), RcppParallel (≥ 5.0.1)
Suggests:	knitr, rmarkdown, testthat
Published:	2024-02-27
DOI:	10.32614/CRAN.package.MADPop
Author:	Martin Lysy [cre, aut], Peter W.J. Kim [aut], Terin Robinson [ctb]
Maintainer:	Martin Lysy <mlysy at uwaterloo.ca>
BugReports:	https://github.com/mlysy/MADPop/issues
License:	GPL-3
URL:	https://github.com/mlysy/MADPop
NeedsCompilation:	yes
SystemRequirements:	GNU make
Materials:	NEWS
CRAN checks:	MADPop results

Documentation:

Reference manual:	MADPop.pdf
Vignettes:	Bayesian Testing of Equal Genotype Proportions between Multiple Populations

Downloads:

Package source:	MADPop_1.1.7.tar.gz
Windows binaries:	r-devel: MADPop_1.1.7.zip, r-release: MADPop_1.1.7.zip, r-oldrel: MADPop_1.1.7.zip
macOS binaries:	r-release (arm64): MADPop_1.1.7.tgz, r-oldrel (arm64): MADPop_1.1.7.tgz, r-release (x86_64): MADPop_1.1.7.tgz, r-oldrel (x86_64): MADPop_1.1.7.tgz
Old sources:	MADPop archive

Linking:

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