https://github.com/mlysy/madpop

MHC Allele-Based Differencing between Populations
https://github.com/mlysy/madpop

Last synced: 3 months ago
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MHC Allele-Based Differencing between Populations

• Host: GitHub
• URL: https://github.com/mlysy/madpop
• Owner: mlysy
• License: gpl-3.0
• Created: 2017-01-14T20:09:08.000Z (about 8 years ago)
• Default Branch: main
• Last Pushed: 2024-02-26T17:23:32.000Z (11 months ago)
• Last Synced: 2024-10-11T19:36:59.430Z (4 months ago)
• Language: R
• Homepage:
• Size: 1.02 MB
• Stars: 1
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: License.md

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README

        
# MADPop: MHC Allele-Based Differencing Between Populations

*Martin Lysy, Peter W.J. Kim, Terin Robinson*

  

  [![R-CMD-check](https://github.com/mlysy/MADPop/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mlysy/MADPop/actions/workflows/R-CMD-check.yaml)

  

---

### 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**](https://mc-stan.org/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:

```r

install.packages("MADPop")

```

To install the latest development version, first install the R package [**devtools**](https://CRAN.R-project.org/package=devtools) then run

```r

devtools::install_github("mlysy/MADPop")

```

### Usage

Please see tutorial [here](https://CRAN.R-project.org/package=MADPop/vignettes/MADPop-quicktut.html) or by running `vignette("MADPop-quicktut")`.