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.

Total

5,012

Last month

1,932

Last week

105

Average per day

64

Daily downloads

Total downloads

Description file content

Type
Package
Package
MADPop
Title
MHC Allele-Based Differencing Between Populations
Version
1.1.2
Date
2018-11-07
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.
License
GPL-3
Depends
R (>= 3.4.0), rstan (>= 2.18.1)
Imports
methods, Rcpp (>= 0.12.0), stats
Suggests
knitr, rmarkdown, testthat
LinkingTo
BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
VignetteBuilder
knitr
SystemRequirements
GNU make
Encoding
UTF-8
LazyData
true
RoxygenNote
6.1.0
NeedsCompilation
yes
Packaged
2018-11-07 18:27:34 UTC; mlysy
Author
Martin Lysy [cre, aut], Peter W.J. Kim [aut], Terin Robinson [ctb]
Maintainer
Martin Lysy
Repository
CRAN
Date/Publication
2018-11-08 16:00:03 UTC

install.packages('MADPop')

1.1.2

9 days ago

Martin Lysy

GPL-3

Depends on

R (>= 3.4.0), rstan (>= 2.18.1)

Imports

methods, Rcpp (>= 0.12.0), stats

Suggests

knitr, rmarkdown, testthat

Discussions