HWAlltests

<code>HWAlltests</code> performs all classical frequentists tests for
 Hardy-Weinberg equilibrium and lists their p-values.

htest

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) <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. The functionality of the package is explained in detail in a related JSS paper <doi:10.18637/jss.v064.i03>.

Jan Graffelman

HardyWeinberg

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Christopher Chang

Xavi Puig

Jan Wigginton

Leonardo Ortoleva

William R. Engels

HWAlltests function

<dl> <dt>x</dt>
<dd>a vector with a set of genotype counts (AA, AB, BB)</dd> <dt>verbose</dt>
<dd>print output if set to TRUE</dd> <dt>include.permutation.test</dt>
<dd>turns on the permutation test if set
 to TRUE</dd> <dt>x.linked</dt>
<dd><code>x.linked=FALSE</code> indicates the marker is
 autosomal (default), and <code>x.linked=TRUE</code> indicates it resides
 on the X-chromosome.</dd></dl>

Arguments

Jan Graffelman <a href="/link/jan.graffelman%40upc.edu?package=HardyWeinberg&version=1.7.8" data-mini-rdoc="HardyWeinberg::jan.graffelman@upc.edu">jan.graffelman@upc.edu</a>

Author

Perform all tests for Hardy-Weinberg equilibrium — HWAlltests

<dl>

 <dt>x</dt>
<dd>a vector with a set of genotype counts (AA, AB, BB)</dd>

 <dt>verbose</dt>
<dd>print output if set to TRUE</dd>

 <dt>include.permutation.test</dt>
<dd>turns on the permutation test if set
 to TRUE</dd>

 <dt>x.linked</dt>
<dd><code>x.linked=FALSE</code> indicates the marker is
 autosomal (default), and <code>x.linked=TRUE</code> indicates it resides
 on the X-chromosome.</dd>

</dl>

Jan Graffelman <a href='mailto:jan.graffelman@upc.edu'>jan.graffelman@upc.edu</a>

HWAlltests: Perform all tests for Hardy-Weinberg equilibrium

Description

Usage

Value

Arguments

Author

Details

See Also

Examples