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'))

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 5 months agofrom:e6d2cfa58c. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-linux	OK	Nov 29 2024

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

Dependencies:BayesFactor bbmle bdsmatrix bitops calibrate caTools circlize cli coda codetools colorspace contfrac corrplot cpp11 data.table deSolve digest dplyr elliptic emdbook fansi farver FNN future generics ggplot2 ggrepel GlobalOptions globals glue gplots gridExtra gtable gtools hypergeo isoband jpeg kernlab KernSmooth ks labeling lattice lifecycle listenv magrittr MASS Matrix MatrixModels mclust mgcv multicool munsell mvtnorm nlme numDeriv parallelly pbapply pillar pkgconfig plyr pracma purrr qqman R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RcppGSL RcppParallel RcppZiggurat Rfast rlang scales shape stringi stringr tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr yarrr

metaGE-vignette

Annaig De Walsche

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

Last update: 2023-08-30
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 1.1.0

metaGE: Meta-Analysis for Detecting Genotype x Environment Associations

metaGE-vignette

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)