HardyWeinberg

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.

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Description file content

Package
HardyWeinberg
Type
Package
Title
Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Version
1.6.2
Date
2019-04-12
Author
Jan Graffelman [aut, cre], Christopher Chang [ctb], Xavi Puig [ctb], Jan Wigginton [ctb]
Maintainer
Jan Graffelman
Depends
R (>= 1.8.0), mice, Rsolnp
Description
Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) , including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
License
GPL (>= 2)
URL
LinkingTo
Rcpp
Imports
Rcpp
NeedsCompilation
yes
Packaged
2019-04-14 18:40:48 UTC; Jan
Repository
CRAN
Date/Publication
2019-04-14 20:53:11 UTC

install.packages('HardyWeinberg')

1.6.2

9 days ago

https://www.r-project.org

Jan Graffelman

GPL (>= 2)

Depends on

R (>= 1.8.0), mice, Rsolnp

Imports

Rcpp

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