LEGIT: Latent Environmental & Genetic InTeraction (LEGIT) Model

Constructs genotype x environment interaction (GxE) models where G is a weighted sum of genetic variants (genetic score) and E is a weighted sum of environments (environmental score) using the alternating optimization algorithm by Jolicoeur-Martineau et al. (2017) <doi:10.48550/arXiv.1703.08111>. This approach has greatly enhanced predictive power over traditional GxE models which include only a single genetic variant and a single environmental exposure. Although this approach was originally made for GxE modelling, it is flexible and does not require the use of genetic and environmental variables. It can also handle more than 2 latent variables (rather than just G and E) and 3-way interactions or more. The LEGIT model produces highly interpretable results and is very parameter-efficient thus it can even be used with small sample sizes (n < 250). Tools to determine the type of interaction (vantage sensitivity, diathesis-stress or differential susceptibility), with any number of genetic variants or environments, are available <doi:10.48550/arXiv.1712.04058>. The software can now produce mixed-effects LEGIT models through the lme4 package.

Version: 1.4.1
Depends: formula.tools, stats, graphics
Imports: pROC, foreach, snow, doSNOW, utils, iterators, Hmisc, grDevices, boot, RColorBrewer, glmnet, lme4, methods
Suggests: knitr, rmarkdown
Published: 2024-01-24
DOI: 10.32614/CRAN.package.LEGIT
Author: Alexia Jolicoeur-Martineau
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau at mail.mcgill.ca>
License: GPL-3
NeedsCompilation: no
Materials: NEWS
CRAN checks: LEGIT results


Reference manual: LEGIT.pdf
Vignettes: Elastic Net
GxE Testing
Latent Environmental & Genetic InTeraction (LEGIT) modelling


Package source: LEGIT_1.4.1.tar.gz
Windows binaries: r-devel: LEGIT_1.4.1.zip, r-release: LEGIT_1.4.1.zip, r-oldrel: LEGIT_1.4.1.zip
macOS binaries: r-release (arm64): LEGIT_1.4.1.tgz, r-oldrel (arm64): LEGIT_1.4.1.tgz, r-release (x86_64): LEGIT_1.4.1.tgz, r-oldrel (x86_64): LEGIT_1.4.1.tgz
Old sources: LEGIT archive


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