MADPop: MHC Allele-Based Differencing Between Populations

Package: MADPop 1.1.6

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.

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

MADPop_1.1.6.tar.gz
MADPop_1.1.6.zip(r-4.7)MADPop_1.1.6.zip(r-4.6)MADPop_1.1.6.zip(r-4.5)
MADPop_1.1.6.tgz(r-4.6-x86_64)MADPop_1.1.6.tgz(r-4.6-arm64)MADPop_1.1.6.tgz(r-4.5-x86_64)MADPop_1.1.6.tgz(r-4.5-arm64)
MADPop_1.1.6.tar.gz(r-4.7-arm64)MADPop_1.1.6.tar.gz(r-4.7-x86_64)MADPop_1.1.6.tar.gz(r-4.6-arm64)MADPop_1.1.6.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MADPop/json (API)

# Install 'MADPop' in R:

install.packages('MADPop', repos = c('https://mlysy.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mlysy/madpop/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

fish215 - Genotypes of lake trout from Ontario, Canada

On CRAN:

cpp

3.70 score 1 stars 9 scripts 245 downloads 5 exports 48 dependencies

Last updated from:d40d77b12f. Checks:12 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	241
linux-devel-x86_64	OK	253
source / vignettes	OK	302
linux-release-arm64	OK	247
linux-release-x86_64	OK	258
macos-release-arm64	OK	146
macos-release-x86_64	OK	304
macos-oldrel-arm64	OK	139
macos-oldrel-x86_64	OK	431
windows-devel	OK	318
windows-release	OK	267
windows-oldrel	OK	324
wasm-release	FAIL	153

Exports:chi2.stat hUM.post LRT.stat UM.eqtest UM.suff

Dependencies:abind backports BH callr checkmate cli cpp11 desc distributional farver generics ggplot2 glue gridExtra gtable inline isoband labeling lifecycle loo magrittr matrixStats numDeriv otel pillar pkgbuild pkgconfig posterior processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan rstantools S7 scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

Bayesian Testing of Equal Genotype Proportions between Multiple Populations

Rendered fromMADPop-quicktut.Rmdusingknitr::rmarkdown

Help page	Topics
(M)HC (A)llele-Based (D)ifferencing between (Pop)ulations	MADPop-package MADPop
Chi-squared test statistic for contingency tables	chi2.stat
Genotypes of lake trout from Ontario, Canada	fish215
Posterior sampling from a hierarchical Unconstrained-Multinomial model	hUM.post
Likelihood ratio test statistic for contingency tables	LRT.stat
Equality tests for two multinomial samples	UM.eqtest
Sufficient statistics for the Unconstrained-Multinomial model	UM.suff

Help page

Topics

(M)HC (A)llele-Based (D)ifferencing between (Pop)ulations

MADPop-package MADPop

Chi-squared test statistic for contingency tables

chi2.stat

Genotypes of lake trout from Ontario, Canada

fish215

Posterior sampling from a hierarchical Unconstrained-Multinomial model

hUM.post

Likelihood ratio test statistic for contingency tables

LRT.stat