RegressionStatTestNA

The function RegressionStatTest compute the statistic and the pvalue of the regression 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

RegressionStatTestNA function

<dl><dt>Covariate</dt>
<dd>A dataset containing the values of one covariate (in columns) in each environment (in rows).</dd>
<dt>CovName</dt>
<dd>The name the covariate.</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 <code>NA</code> configuration for all marker</dd>
<dt>Configs.list</dt>
<dd>A vector containing the NA configurations present in the dataset</dd></dl>

Arguments

Compute the pvalue of the regression test in presence of missing values. — RegressionStatTestNA

<dl>

<dt>Covariate</dt>
<dd>A dataset containing the values of one covariate (in columns) in each environment (in rows).</dd>


<dt>CovName</dt>
<dd>The name the covariate.</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 <code>NA</code> configuration for all marker</dd>


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

</dl>

RegressionStatTestNA: Compute the pvalue of the regression test in presence of missing values.

Description

Usage

Value

Arguments