README.md
In mlysy/MADPop: MHC Allele-Based Differencing Between Populations
MADPop: MHC Allele-Based Differencing Between Populations
Martin Lysy, Peter W.J. Kim, Terin Robinson
Description
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.
Installation
To install the latest R release:
install.packages("MADPop")
To install the latest development version, first install the R package devtools then run
devtools::install_github("mlysy/MADPop")
Usage
Please see tutorial here or by running vignette("MADPop-quicktut").
mlysy/MADPop documentation built on Feb. 28, 2024, 12:29 p.m.
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MADPop: MHC Allele-Based Differencing Between Populations
Martin Lysy, Peter W.J. Kim, Terin Robinson
Description
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.
Installation
To install the latest R release:
install.packages("MADPop")
To install the latest development version, first install the R package devtools then run
devtools::install_github("mlysy/MADPop")
Usage
Please see tutorial here or by running vignette("MADPop-quicktut").
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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