ReadData

This function read the one file, select interesting columns and rename them.

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

ReadData function

<dl><dt>ListN</dt>
<dd>The name of the list of files where the file to read belongs or NULL if there is only one list of files</dd>
<dt>FileN</dt>
<dd>The name of the file to read</dd>
<dt>VarN</dt>
<dd>A named list containing the column names in the file corresponding to the variables below: MARKER, CHR, POS, EFFECT, PVAL. (optional: FREQ, ALLELE0, ALLELE1)</dd>
<dt>MinFreq</dt>
<dd>A numeric value allowing to filter to keep markers with MAF &gt; MinFreq</dd></dl>

Arguments

ReadData — ReadData

<dl>

<dt>ListN</dt>
<dd>The name of the list of files where the file to read belongs or NULL if there is only one list of files</dd>


<dt>FileN</dt>
<dd>The name of the file to read</dd>


<dt>VarN</dt>
<dd>A named list containing the column names in the file corresponding to the variables below: MARKER, CHR, POS, EFFECT, PVAL. (optional: FREQ, ALLELE0, ALLELE1)</dd>


<dt>MinFreq</dt>
<dd>A numeric value allowing to filter to keep markers with MAF &gt; MinFreq</dd>

</dl>

ReadData: ReadData

Description

Usage

Value

Arguments