ContrastStatTest.NA

The function ContrastStatTest compute the statistic of the contrast test.

Provides functions to perform all steps of genome-wide
association meta-analysis for studying Genotype x Environment
interactions, from collecting the data to the manhattan plot.  The
procedure accounts for the potential correlation between studies. In
addition to the Fixed and Random models, one can investigate the
relationship between QTL effects and some qualitative or quantitative
covariate via the test of contrast and the meta-regression,
respectively.  The methodology is available from: (De Walsche, A., et
al. (2025) \doi{10.1371/journal.pgen.1011553}).

Annaïg De Walsche

metaGE

Meta-Analysis for Detecting Genotype x Environment Associations

Tristan Mary-Huard

ContrastStatTest.NA function

<dl><dt>Incidence</dt>
<dd>A matrix of incidence, as obtained from metaGE.incidence.</dd>
<dt>Contrast</dt>
<dd>A matrix of contrast, if NULL the identity matrix is used. (<code>NULL</code> by default)</dd>
<dt>Zmat</dt>
<dd>A matrix containing the Zscores of all markers (in rows) in each environment (in columns).</dd>
<dt>MatCorr</dt>
<dd>The inter-environments correlation matrix. Can be computed using <code>metaGE.cor()</code>.</dd>
<dt>Data</dt>
<dd>A dataset containing the effect, the pvalues and the na configuration for all marker</dd>
<dt>Configs.list</dt>
<dd>A vector containing the <code>NA</code> configurations present in the dataset</dd>
<dt>IncidenceName</dt>
<dd>The name of the incidence.</dd></dl>

Arguments

Compute the statistic of the contrast test in presence of missing values — ContrastStatTest.NA

<dl>

<dt>Incidence</dt>
<dd>A matrix of incidence, as obtained from metaGE.incidence.</dd>


<dt>Contrast</dt>
<dd>A matrix of contrast, if NULL the identity matrix is used. (<code>NULL</code> by default)</dd>


<dt>Zmat</dt>
<dd>A matrix containing the Zscores of all markers (in rows) in each environment (in columns).</dd>


<dt>MatCorr</dt>
<dd>The inter-environments correlation matrix. Can be computed using <code>metaGE.cor()</code>.</dd>


<dt>Data</dt>
<dd>A dataset containing the effect, the pvalues and the na configuration for all marker</dd>


<dt>Configs.list</dt>
<dd>A vector containing the <code>NA</code> configurations present in the dataset</dd>


<dt>IncidenceName</dt>
<dd>The name of the incidence.</dd>

</dl>

ContrastStatTest.NA: Compute the statistic of the contrast test in presence of missing values

Description

Usage

Value

Arguments