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) . 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 Although this approach was originally made for GxE modelling, it is flexible and does not require the use of genetic and environmental variables.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).


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Reference manual

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install.packages("LEGIT")

1.1.1 by Alexia Jolicoeur-Martineau, 17 hours ago


Browse source code at https://github.com/cran/LEGIT


Authors: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>


Documentation:   PDF Manual  


GPL-3 license


Imports pROC, foreach, snow, doSNOW, utils, iterators

Depends on formula.tools, stats

Suggests knitr, rmarkdown


See at CRAN