Meta-Analysis for Detecting Genotype x Environment Associations
Computation of the autocorrelation
Check and reformat the matrix of contrast
Check and reformat the matrix of incidence
ReadData
Compute the pvalue of the meta-regression test.
Compute the pvalue of the regression test in presence of missing value...
Computation of the significative regions
Computation of the significance threshold
Compute the statistic of the contrast test in presence of missing valu...
Compute the statistic of the contrast test.
FastKerFdr
GetH0Items
Computation of the lindley process from scores.
LLikelihoodT_vect
Drawing a QQplot
metaGE: Meta-Analysis for Detecting Genotype x Environment Association...
Collect the results of GWAS data from different files
Infer inter-environment correlation matrix
Meta-analysis procedure: Fixed or Random effect.
Draw the heatmap to see markers effects across environments.
Meta-analysis test for Genotype x Environment interactions: Contrast o...
Create the matrix of incidence.
Compute the local score from a set of pvalues.
Draw the Manhattan plot.
Display visual checks of pvalues.
Plot the z-score of a marker according to a covariate.
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. (2023) \doi{10.1101/2023.03.01.530237}).