simPheno: Fonction to simulate phenotype values

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

Description

The fonction simulate a quantitative phenotype assuming a gene-structure among the SNPs.

Usage

simPheno(X, listGenes, MainEff, GenePair, model = "SNPproduct",
  pvBeta = c(2, 2), pvGamma = c(2, 2), r2 = 0.2, causalSNPnb,
  causalSNPportion = NULL, beta0 = 0)

Arguments

X	a matrix where columns are SNPs and rows are individuals.
listGenes	a list that indicate the names of the SNPs composing each gene.
MainEff	a vector containing the names of genes having main effects.
GenePair	a vector containing the names of genes having interaction effects. The size of the vector GenePair has to be an even number, pairs being defined with the gene taken two by two along the vector.
model	the model to consider to simulate interaction effects, either "SNPproduct" or "PCproduct".
pvBeta	numerical vector of possible values for main effects regression coefficients.
pvGamma	numerical vector of possible values for interaction effects regression coefficients.
r2	numeric value between 0 and 1. Coefficient of determination.
causalSNPnb	numerical value. number of SNP in each gene to considered as causal.
causalSNPportion	value between 0 and 1. Portion of SNP in each gene to considered as causal (if causalSNPnb is NULL).
beta0	numeric value; intercept coefficient. Default 0.

Value

Returns a list including:

y	vector of simulated phenotype continuous values
G	matrix of the simulated main effects.
GG	matrix of the simulated interaction effects.
R2T	numerical value for the coefficient of determination R2 when considering the model containing simulated main and interaction effects.
R2I	numerical value for the coefficient of determination R2 when considering the model containing only simulated interaction effects.
R2S	numerical value for the coefficient of determination R2 when considering the model containing only simulated main effects.
caract	a list with the caracteristic elements of the simulation.

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