simGeno: Fonction to simulate genotype data

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

Description

The fonction create a SNP data set structured by genes with genotypes coded by 1, 2 and 3.

Usage

simGeno(N = 600, corr = 0.8, sizeGenesMain, sizeGenesPair, sizeGenesRemain,
  SameMainPair, MAFcausalSNP = NULL, causalSNPnb, causalSNPportion,
  AllMainPair = TRUE, minMAF = 0.05, maxMAF = 0.5)

Arguments

N	integer; number of individuals.
corr	numeric value between 0 and 1. Correlation level among the SNPs within each gene.
sizeGenesMain	a vector of integers specifying the sizes of the genes having main effects.
sizeGenesPair	a vector of integers specifying the sizes of the genes having interaction effects. The size of the vector has to be an even number, pairs being defined with the gene taken two by two along the vector.
sizeGenesRemain	a vector of integers specifying the sizes of the genes having none effects.
SameMainPair	logical. If TRUE, genes with interation effects will also have main effects
MAFcausalSNP	MAF value for causal SNPs
causalSNPnb	integer. 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).
AllMainPair	logical. If FALSE, only the first gene of each interaction pair will have a main effect. SameMainPair has to be TRUE.
minMAF	minimum value of the Minor Allele Frequency. Default 0.05.
maxMAF	maximum value of the Minor Allele Frequency. Default 0.5.

Value

Returns a list including:

X	a matrix where columns are SNPs and rows are individuals.
listGenesSNP	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.
MAF	a vector that give the minor allele frequency observed for each simulated SNP.

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