Package: metaGE 1.1.0

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. (2023) \doi{10.1101/2023.03.01.530237}).

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

metaGE_1.1.0.tar.gz
metaGE_1.1.0.tar.gz(r-4.5-noble)metaGE_1.1.0.tar.gz(r-4.4-noble)
metaGE_1.1.0.tgz(r-4.4-emscripten)metaGE_1.1.0.tgz(r-4.3-emscripten)
metaGE.pdf |metaGE.html
metaGE/json (API)

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

Peer review:

Datasets:
  • envDesc - Description of the environments.
  • metaData - Results of different GWAS.

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 291 downloads 10 exports 86 dependencies

Last updated 4 months agofrom:e6d2cfa58c. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-linuxOKNov 29 2024

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

Dependencies:BayesFactorbbmlebdsmatrixbitopscalibratecaToolscirclizeclicodacodetoolscolorspacecontfraccorrplotcpp11data.tabledeSolvedigestdplyrellipticemdbookfansifarverFNNfuturegenericsggplot2ggrepelGlobalOptionsglobalsgluegplotsgridExtragtablegtoolshypergeoisobandjpegkernlabKernSmoothkslabelinglatticelifecyclelistenvmagrittrMASSMatrixMatrixModelsmclustmgcvmulticoolmunsellmvtnormnlmenumDerivparallellypbapplypillarpkgconfigplyrpracmapurrrqqmanR6RColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratRfastrlangscalesshapestringistringrtibbletidyrtidyselectutf8vctrsviridisviridisLitewithryarrr

metaGE-vignette

Rendered frommetaGE-vignette.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-08-30
Started: 2023-08-30