Meta-Analysis for Detecting Genotype x Environment Associations

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Documentation for package ‘metaGE’ version 1.0.3

• 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