JPTtriallelicsChrX

<code>JPTtriallelicsChrX</code> contains five selected tri-allelic variants on the
X chromosome from the Japanese sample of the 1000 genomes project.

datasets

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

JPTtriallelicsChrX function

A data frame with 5 observations on the following 12 variables.<dl>
 <dt><code>id</code></dt>
<dd>Identifier of the polymorphism</dd> <dt><code>pos</code></dt>
<dd>Position of the polymorphism in base pairs</dd> <dt><code>chr</code></dt>
<dd>Chromosome</dd> <dt><code>A</code></dt>
<dd>Number of males with A genotype</dd> <dt><code>B</code></dt>
<dd>Number of males with B genotype</dd> <dt><code>C</code></dt>
<dd>Number of males with C genotype</dd> <dt><code>AA</code></dt>
<dd>Number of AA females</dd> <dt><code>AB</code></dt>
<dd>Number of AB females</dd> <dt><code>AC</code></dt>
<dd>Number of AC females</dd> <dt><code>BB</code></dt>
<dd>Number of BB females</dd> <dt><code>BC</code></dt>
<dd>Number of BC females</dd> <dt><code>CC</code></dt>
<dd>Number of CC females</dd> 
</dl>

Format

Tri-allelic variants on the X-chromosome of the Japanese (JPT) sample of the 1000 genomes project — JPTtriallelicsChrX

A data frame with 5 observations on the following 12 variables.<dl>
 <dt><code>id</code></dt>
<dd>Identifier of the polymorphism</dd>

 <dt><code>pos</code></dt>
<dd>Position of the polymorphism in base pairs</dd>

 <dt><code>chr</code></dt>
<dd>Chromosome</dd>

 <dt><code>A</code></dt>
<dd>Number of males with A genotype</dd>

 <dt><code>B</code></dt>
<dd>Number of males with B genotype</dd>

 <dt><code>C</code></dt>
<dd>Number of males with C genotype</dd>

 <dt><code>AA</code></dt>
<dd>Number of AA females</dd>

 <dt><code>AB</code></dt>
<dd>Number of AB females</dd>

 <dt><code>AC</code></dt>
<dd>Number of AC females</dd>

 <dt><code>BB</code></dt>
<dd>Number of BB females</dd>

 <dt><code>BC</code></dt>
<dd>Number of BC females</dd>

 <dt><code>CC</code></dt>
<dd>Number of CC females</dd>

 
</dl>

JPTtriallelicsChrX: Tri-allelic variants on the X-chromosome of the Japanese (JPT) sample of the 1000 genomes project

Description

Usage

Arguments

Format

References

Examples