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: |
1.1.2 |
| Depends: |
R (≥ 3.4.0), rstan (≥ 2.18.1) |
| Imports: |
methods, Rcpp (≥ 0.12.0), stats |
| LinkingTo: |
BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0) |
| Suggests: |
knitr, rmarkdown, testthat |
| Published: |
2018-11-08 |
| Author: |
Martin Lysy [cre, aut],
Peter W.J. Kim [aut],
Terin Robinson [ctb] |
| Maintainer: |
Martin Lysy <mlysy at uwaterloo.ca> |
| License: |
GPL-3 |
| NeedsCompilation: |
yes |
| SystemRequirements: |
GNU make |
| CRAN checks: |
MADPop results |