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metaGE (version 1.2.2)

Meta-Analysis for Detecting Genotype x Environment Associations

Description

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}).

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Version

Install

install.packages('metaGE')

Monthly Downloads

319

Version

1.2.2

License

GPL-3

Maintainer

Annaïg De Walsche

Last Published

July 21st, 2025

Functions in metaGE (1.2.2)

metaGE.incidence

Create the matrix of incidence.

ContrastStatTest

Compute the statistic of the contrast test.

Draw the heatmap to see markers effects across environments.

Description of the environments.

metaGE.manhattan

Draw the Manhattan plot.

Computation of the lindley process from scores.

metaGE.pvalplot

Display visual checks of pvalues.

Compute the local score from a set of pvalues.

Meta-analysis test for Genotype x Environment interactions: Contrast or Regression.

Plot the z-score of a marker according to a covariate.

Check and reformat the matrix of incidence

ContrastStatTest.NA

Compute the statistic of the contrast test in presence of missing values

LLikelihoodT_vect

LLikelihoodT_vect

Check and reformat the matrix of contrast

Drawing a QQplot

RegressionStatTest

Compute the pvalue of the meta-regression test.

Collect the results of GWAS data from different files

Meta-analysis procedure: Fixed or Random effect.

Results of different GWAS.

Infer inter-environment correlation matrix

Computation of the significative regions

metaGE: Meta-Analysis for Detecting Genotype x Environment Associations

Computation of the significance threshold

RegressionStatTestNA

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

Computation of the autocorrelation