Package: metaGE 1.2.1

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_1.2.1.tar.gz
metaGE_1.2.1.tar.gz(r-4.5-noble)metaGE_1.2.1.tar.gz(r-4.4-noble)
metaGE_1.2.1.tgz(r-4.4-emscripten)metaGE_1.2.1.tgz(r-4.3-emscripten)
metaGE.pdf |metaGE.html✨
metaGE/json (API)

# Install 'metaGE' in R:
install.packages('metaGE', repos = 'https://cloud.r-project.org')
Datasets:
  • envDesc - Description of the environments.
  • metaData - Results of different GWAS.

On CRAN:

Conda:

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

2.30 score 530 downloads 10 exports 86 dependencies

Last updated 1 months agofrom:c338492917. Checks:3 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 25 2025
R-4.5-linuxOKMar 25 2025
R-4.4-linuxOKMar 25 2025

Exports:metaGE.collectmetaGE.cormetaGE.fitmetaGE.heatmapmetaGE.incidencemetaGE.lscoremetaGE.manhattanmetaGE.pvalplotmetaGE.regplotmetaGE.test

Dependencies:BayesFactorbbmlebdsmatrixbitopscalibratecaToolscirclizeclicodacodetoolscolorspacecontfraccorrplotcpp11data.tabledeSolvedigestdplyrellipticemdbookfansifarverFNNfurrrfuturegenericsggplot2ggrepelGlobalOptionsglobalsgluegplotsgridExtragtablegtoolshypergeoisobandjpegkernlabKernSmoothkslabelinglatticelifecyclelistenvmagrittrMASSMatrixMatrixModelsmclustmgcvmulticoolmunsellmvtnormnlmenumDerivparallellypbapplypillarpkgconfigplyrpracmapurrrqqmanR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRfastrlangscalesshapestringistringrtibbletidyrtidyselectutf8vctrsviridisviridisLitewithryarrrzigg

metaGE-vignette

Annaig De Walsche

Rendered frommetaGE-vignette.Rmdusingknitr::rmarkdownon Mar 25 2025.

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

Citation

To cite package ‘metaGE’ in publications use:

De Walsche A, Mary-Huard T (2025). metaGE: Meta-Analysis for Detecting Genotype x Environment Associations. R package version 1.2.1, https://CRAN.R-project.org/package=metaGE.

Corresponding BibTeX entry: 

  @Manual{,
    title = {metaGE: Meta-Analysis for Detecting Genotype x Environment
      Associations},
    author = {Annaïg {De Walsche} and Tristan Mary-Huard},
    year = {2025},
    note = {R package version 1.2.1},
    url = {https://CRAN.R-project.org/package=metaGE},
  }