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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 Although this approach was originally made for GxE modelling, it is flexible and does not require the use of genetic and environmental variables.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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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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