BuiltEpiVar: Fonction to create interaction variable.

In vstanislas/GGEE: R Package for the Group Lasso Gene-Gene Eigen Epistasis (G-GEE) Method

Description

The fonction create interaction variable from a genetic data set structured by group.

Usage

BuiltEpiVar(X, Y, method, listGenesSNP, nbcomp = 2, idSubs)

Arguments

X	a genotype matrix where columns are genetic markers and rows are samples.
Y	phenotype values can be logical (1/0) or numericGLmodel.
method	method to consider for interactions variable construction : "GGEE": Compute the gene-gene interaction variables for each gene pair by finding its Eigen-epistasis Component defined as the linear combination of Gene SNPs having the highest correlation with the phenotype. "PCA": Compute the gene-gene interaction variables for each gene pair with Principal Component Analysis. "PLS": Compute the gene-gene interaction variables for each gene pair with Partial Least Square. "CCA": Compute the gene-gene interaction variables for a given gene pair with Canonical Correlation Analysis.
listGenesSNP	list containing the names of genetic marker for each group.
nbcomp	number of components to consider to built interaction variables for "PCA", "PLS" and "CCA" methods (2 by default).

Value

Returns a list including:

XInt	a matrix where columns are interaction variables and rows are samples.
interLength	a vector that indicate the number of interaction variable for each gene couple.

vstanislas/GGEE documentation built on May 28, 2021, 12:50 p.m.