HWClrPlot

<code>HWClrPlot</code> creates a scatter plot of the centred log-ratio coordinates of
 bi-allelic genetic markers. Hardy-Weinberg equilibrium is indicated by
 a straigh line in the plot.

aplot

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

HWClrPlot function

<dl> <dt>X</dt>
<dd>A matrix of genotype counts (columns AA, AB, BB)</dd> <dt>zeroadj</dt>
<dd>Zero-adjustment parameter. Zero counts in the count
 matrix are substituted by <code>zeroadj</code> which is 0.5 by default.</dd></dl>

Arguments

Jan Graffelman (jan.graffelman@upc.edu)

Author

Plot genetic markers in centred log-ratio coordinates — HWClrPlot

<dl>

 <dt>X</dt>
<dd>A matrix of genotype counts (columns AA, AB, BB)</dd>

 <dt>zeroadj</dt>
<dd>Zero-adjustment parameter. Zero counts in the count
 matrix are substituted by <code>zeroadj</code> which is 0.5 by default.</dd>

</dl>

HWClrPlot: Plot genetic markers in centred log-ratio coordinates

Description

Usage

Value

Arguments

Author

References

See Also

Examples