LLikelihoodT_vect

This function compute the values of loglikelihood for all markers.

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

LLikelihoodT_vect function

<dl><dt>Zmat</dt>
<dd>A matrix containing the Zscores of all markers (in rows) in each environment (in columns)</dd>
<dt>Delta</dt>
<dd>A vector containing the diagonal coefficients of the diagonal matrix obtained by the diagonalization of the correlation matrix</dd>
<dt>P</dt>
<dd>Matrix such that MatCorr = P Delta t(P), with Delta diagonal</dd>
<dt>Mu</dt>
<dd>A vector containing the average effect of the markers</dd>
<dt>Tau</dt>
<dd>A vector containing the heterogeneity between environments of the markers</dd></dl>

Arguments

LLikelihoodT_vect — LLikelihoodT_vect

<dl>

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


<dt>Delta</dt>
<dd>A vector containing the diagonal coefficients of the diagonal matrix obtained by the diagonalization of the correlation matrix</dd>


<dt>P</dt>
<dd>Matrix such that MatCorr = P Delta t(P), with Delta diagonal</dd>


<dt>Mu</dt>
<dd>A vector containing the average effect of the markers</dd>


<dt>Tau</dt>
<dd>A vector containing the heterogeneity between environments of the markers</dd>

</dl>

LLikelihoodT_vect: LLikelihoodT_vect

Description

Usage

Value

Arguments