# Meta-Analysis for Detecting Genotype x Environment Associations

## Documentation for package ‘metaGE’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

autocor | Computation of the autocorrelation
CheckContrast | Check and reformat the matrix of contrast
CheckIncidence | Check and reformat the matrix of incidence
ContrastStatTest | Compute the statistic of the contrast test.
ContrastStatTest.NA | Compute the statistic of the contrast test in presence of missing values
envDesc | Description of the environments.
FastKerFdr | FastKerFdr
GetH0Items | GetH0Items
lindley | Computation of the lindley process from scores.
LLikelihoodT_vect | LLikelihoodT_vect
MakeQQplot | Drawing a QQplot
metaData | Results of different GWAS.
metaGE.collect | Collect the results of GWAS data from different files
metaGE.cor | Infer inter-environment correlation matrix
metaGE.fit | Meta-analysis procedure: Fixed or Random effect.
metaGE.heatmap | Draw the heatmap to see markers effects across environments.
metaGE.incidence | Create the matrix of incidence.
metaGE.lscore | Compute the local score from a set of pvalues.
metaGE.manhattan | Draw the Manhattan plot.
metaGE.pvalplot | Display visual checks of pvalues.
metaGE.regplot | Plot the z-score of a marker according to a covariate.
metaGE.test | Meta-analysis test for Genotype x Environment interactions: Contrast or Regression.
ReadData | ReadData
RegressionStatTest | Compute the pvalue of the meta-regression test.
RegressionStatTestNA | Compute the pvalue of the regression test in presence of missing values.
sig_sl | Computation of the significative regions
thresUnif | Computation of the significance threshold