qqunif

<code>qqunif</code> makes a Q-Q plot against a uniform distribution for the supplied data vector.

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

qqunif function

<dl> <dt>x</dt>
<dd>The data vector</dd> <dt>logplot</dt>
<dd>If <code>logplot</code> is set to true, then the log10 of the
 p-values will be used in the plot. If not, untransformed p-values will
 be used.</dd> <dt>lbs</dt>
<dd>A vector of labels for the points in the Q-Q plot</dd> <dt>texton</dt>
<dd>Logical indicating whether labels should be plotted or not</dd> <dt>xylim</dt>
<dd>Shared upper limit x and y axis in the plot</dd> <dt>main</dt>
<dd>Title for the plot</dd> <dt>plotline</dt>
<dd>Setting <code>plotline=0</code> plots a (0,1) line; <code>plotline=1</code> plots a robust fit,</dd> <dt>xlab</dt>
<dd>label for the x axis</dd> <dt>ylab</dt>
<dd>label for the y axis</dd> <dt>colvec</dt>
<dd>vector with colours for the points in the QQ plot</dd> <dt>colline</dt>
<dd>colour for the line in the plot</dd> <dt>...</dt>
<dd>Any additional arguments for the <code>plot</code> instruction</dd></dl>

Arguments

Jan Graffelman (jan.graffelman@upc.edu)

Author

Q-Q plot for a uniform distribution. — qqunif

<dl>

 <dt>x</dt>
<dd>The data vector</dd>

 <dt>logplot</dt>
<dd>If <code>logplot</code> is set to true, then the log10 of the
 p-values will be used in the plot. If not, untransformed p-values will
 be used.</dd>

 <dt>lbs</dt>
<dd>A vector of labels for the points in the Q-Q plot</dd>

 <dt>texton</dt>
<dd>Logical indicating whether labels should be plotted or not</dd>

 <dt>xylim</dt>
<dd>Shared upper limit x and y axis in the plot</dd>

 <dt>main</dt>
<dd>Title for the plot</dd>

 <dt>plotline</dt>
<dd>Setting <code>plotline=0</code> plots a (0,1) line; <code>plotline=1</code> plots a robust fit,</dd>

 <dt>xlab</dt>
<dd>label for the x axis</dd>

 <dt>ylab</dt>
<dd>label for the y axis</dd>

 <dt>colvec</dt>
<dd>vector with colours for the points in the QQ plot</dd>

 <dt>colline</dt>
<dd>colour for the line in the plot</dd>

 <dt>...</dt>
<dd>Any additional arguments for the <code>plot</code> instruction</dd>

</dl>

qqunif: Q-Q plot for a uniform distribution.

Description

Usage

Value

Arguments

Author

See Also

Examples