Package: metaGE 1.2.2

Annaïg De Walsche

metaGE: Meta-Analysis for Detecting Genotype x Environment Associations

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}).

Authors:Annaïg De Walsche [aut, cre], Tristan Mary-Huard [aut]

metaGE_1.2.2.tar.gz
metaGE_1.2.2.tar.gz(r-4.7-any)metaGE_1.2.2.tar.gz(r-4.6-any)
metaGE_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
metaGE/json (API)

# Install 'metaGE' in R:

install.packages('metaGE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

envDesc - Description of the environments.
metaData - Results of different GWAS.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 1 scripts 283 downloads 10 exports 71 dependencies

Last updated from:6643b4cefa. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	226
source / vignettes	OK	237
linux-release-x86_64	OK	250
wasm-release	OK	146

Exports:metaGE.collect metaGE.cor metaGE.fit metaGE.heatmap metaGE.incidence metaGE.lscore metaGE.manhattan metaGE.pvalplot metaGE.regplot metaGE.test

Dependencies:bbmle bdsmatrix bitops calibrate caTools cli coda codetools corrplot cpp11 data.table digest dplyr emdbook farver FNN furrr future generics ggplot2 ggrepel globals glue gplots gridExtra gtable gtools isoband kernlab KernSmooth ks labeling lattice lifecycle listenv magrittr MASS Matrix mclust mgcv multicool mvtnorm nlme numDeriv parallelly pillar pkgconfig plyr pracma purrr qqman R6 RColorBrewer Rcpp RcppArmadillo RcppParallel Rfast rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr zigg

metaGE-vignette

Rendered frommetaGE-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-02-22
Started: 2023-08-30

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

Package: metaGE 1.2.2

metaGE: Meta-Analysis for Detecting Genotype x Environment Associations

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)