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) . Alternating optimization is an iterative process where the genetic score weights, the environmental score weights, and the main model parameters are estimated in turn assuming the other parameters to be constant. This approach has greatly enhanced predictive power over traditional GxE models which include only a single genetic variant and a single environmental exposure. Gene x gene interactions (GxG) and environment x environment interactions (ExE) can be incorporated into the genetic and environmental scores. Any standard model formula can be used, it doesn't have to be a two-way interaction model. Although this approach was made for GxE modelling, the genetic score doesn't need to contain genetic variables and the environmental score doesn't need to contain environmental variables, therefore this approach is highly flexible.


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Reference manual

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install.packages("LEGIT")

1.0.1 by Alexia Jolicoeur-Martineau, 4 days 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

Depends on formula.tools, stats

Suggests knitr, rmarkdown


See at CRAN