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 |