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
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MADPop.pdf |MADPop.html✨
MADPop/json (API)
NEWS

# 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:

Conda:

cpp

3.70 score 1 stars 8 scripts 265 downloads 5 exports 53 dependencies

Last updated 1 years agofrom:d40d77b12f. Checks:4 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 23 2025
R-4.5-win-x86_64NOTEFeb 23 2025
R-4.5-mac-x86_64OKFeb 23 2025
R-4.5-mac-aarch64OKFeb 23 2025
R-4.5-linux-x86_64OKFeb 23 2025
R-4.4-win-x86_64NOTEFeb 23 2025
R-4.4-mac-x86_64NOTEFeb 23 2025
R-4.4-mac-aarch64NOTEFeb 23 2025
R-4.3-win-x86_64NOTEFeb 23 2025
R-4.3-mac-x86_64NOTEFeb 23 2025
R-4.3-mac-aarch64NOTEFeb 23 2025

Exports:chi2.stathUM.postLRT.statUM.eqtestUM.suff

Dependencies:abindbackportsBHcallrcheckmateclicolorspacedescdistributionalfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr

Bayesian Testing of Equal Genotype Proportions between Multiple Populations

Martin Lysy, Wookjung P. Kim, Terin Robinson

Rendered fromMADPop-quicktut.Rmdusingknitr::rmarkdownon Feb 23 2025.

Last update: 2022-08-19
Started: 2016-12-18