SampleGGInter: Simulation of samples under a gene-gene interaction model

In fhebert/GeneGeneInteractions2: Global tests for the detection of gene-gene interaction effects on binary phenotypes

Description

SampleGGInter is used to create a sample of genotype values for two genes and of binary phenotype values. The phenotype is generated conditionally to the genes using a logistic model.

Usage

SampleGGInter(X1, X2, mu, alpha, I.alpha, beta, I.beta, gamma, I.gamma, n0, n1)

Arguments

X1	a N x p1 matrix of genotypes (coded as 0/1/2) for a given gene for a population
X2	a N x p2 matrix of genotypes (coded as 0/1/2) for a given gene for a population
mu	the intercept of the logistic model
alpha	the vector of parameters for the main effects for the first gene
I.alpha	the vector of coordinates corresponding to the coefficients in alpha
beta	the vector of parameters for the main effects for the second gene
I.beta	the vector of coordinates corresponding to the coefficients in beta
gamma	a K x 4 matrix or a vector of length K of gene-gene interaction effects parameters. If it is a K x 4 matrix Each row is a vector of parameters for a pair of SNPs having an interaction effect and a dummy coding of the SNPs is used. The four parameters in a row correspond to the heterozygous/heterozygous, heterozygous/homozygous, homozygous/heterozygous and homozygous/homozygous configurations, respectively. If it is a vector, each coordinate is the interaction parameter for a pair of SNPs having an interaction effect. In this case, a continuous coding is used and the interaction effect is multiplicative
I.gamma	a K x 2 matrix of coordinates for the interacting SNPs. Each row is a pair of SNPs. For a given row (i,j), the i-th SNP of the first gene and the j-th SNP of the second gene have an interaction effect on the phenotype. The interaction parameters for the pair of SNPs in the k-th row of I.gamma are given by the k-th row (or coordinate) of gamma
n0	the desired number of controls
n1	the desired number of cases

Value

A list with 3 elements:

SNP1	the sample matrix of genotypes for the first gene
SNP2	the sample matrices of genotypes for the second gene
Y	the vector of phenotype values

fhebert/GeneGeneInteractions2 documentation built on May 19, 2019, 12:36 a.m.