HardyWeinberg-package: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

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. The functionality of the package is explained in detail in a related paper (Graffelman, 2015).

Details

Package:	HardyWeinberg
Type:	Package
Version:	1.7.7
Date:	2024-03-31
License:	GPL Version 2 or later.

With function HWTernaryPlot one can create ternary plots with acceptance regions for HWE. Several routines implement statistical tests for HWE such as HWChisq, HWExact, HWLratio and HWPerm. Bayesian procedures are available using HWPosterior. Aikaike information criterion for various scenarios can be calculated with HWAIC. Power computations are possible with HWPower.

Author(s)

Jan Graffelman

Maintainer: Jan Graffelman <[e-mail]>

References

Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates, Massachusetts.

Graffelman, J. and Morales, J. (2008) Graphical Tests for Hardy-Weinberg Equilibrium Based on the Ternary Plot. Human Heredity 65(2):77-84.

Graffelman, J. (2015) Exploring Diallelic Genetic Markers: The HardyWeinberg Package. Journal of Statistical Software 64(3): 1-23. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v064.i03")}.

Graffelman, J. and Weir, B.S. (2016) Testing for Hardy-Weinberg equilibrium at bi-allelic genetic markers on the X chromosome. Heredity 116(6): 558-568. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/hdy.2016.20")} Nature Publishing Group.

Hardy, G.H. (1908) Mendelian Proportions in a Mixed Population. Science 28(706): 49-50.

Weinberg, W. (1908) On the Demonstration of Heredity in Man. In: Papers on Human Genetics. S. H. Boyer (Ed.) Englewood Cliffs, NJ:Prentice Hall, translated, 1963.

Examples

library(HardyWeinberg)

# draw random SNPs from a population that is in HWE

set.seed(123)

m <- 100 # number of markers
n <- 100 # sample size

X <- HWData(n,m)
out <- HWTernaryPlot(X,100,region=1,vertex.cex=2,signifcolour=TRUE)

HardyWeinberg documentation built on May 29, 2024, 6:17 a.m.