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R Package for the Group Lasso Gene-Gene Eigen Epistasis (G-GEE) Method
R C++
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DESCRIPTION
GGEE.Rproj
NAMESPACE
README.md

README.md

GGEE

GGEE implements the group lasso Gene-Gene Eigen Epistasis (G-GEE) method for detecting epistasis at the gene level. The proposed functions allow to compute interaction variables for each pair and to fit a general model with a Group Lasso penalty. The package allows to generate gene structured genotype data and continuous phenotype.

Installation

The package can be installed from github:

# install.packages("devtools")
devtools::install_github("vstanislas/GGEE")

GGEE uses several functions from the package ridgeAdap which can also be installed from github:

devtools::install_github("jbecu/ridgeAdap")

Some functions of GGEE use C++ code. On Linux compilation can be interupt depending on the g++ version. The solution is to create a .R/Makevars file in your home directory that contains:

CXXFLAGS= -std=c++11

Examples and descriptions

A detailled example can be find in GGEEvignette.pdf

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