SampleSNPPhenotype: Simulation of a sample of genotype and binary phenotype...

In fhebert/SNPSetSimulations: Simulation of genotypic profiles and binary phenotypes for GWAS

Simulation of a sample of genotype and binary phenotype values

Description

SampleSNPPhenotype is used to generate a sample of genotype values for a gene and of phenotype values. The phenotype is generated conditionally to the gene using a logistic model.

Usage

SampleSNPPhenotype(X, beta0, beta, I, n0, n1, U = NULL, alpha = NULL,
  mod = rep("A", length(I)))

Arguments

X	a N x p matrix of genotype values (coded as 0/1/2) for a given gene for a population
beta0	the intercept of the logistic model
beta	the vector of effect parameters for the logistic model
I	the vector of coordinates corresponding to the coefficients in beta
n0	the desired number of controls
n1	the desired number of cases
U	an optional matrix of covariates profiles
alpha	an optional vector of covariates effects parameters
mod	an optional vector of characters specifying the genetic association model for each SNP position given in I. Possibles values: "A" (additive model), "D" (dominant) and "R" (recessive). Models can be combined (causal SNPs can be associated to the phenotype with different models).

Value

A list containing 3 elements:

SNP	the sample matrix of genotypic profiles
Y	the vector of phenotype values
Covariates	the sample matrix of covariates profiles (if any)

fhebert/SNPSetSimulations documentation built on Jan. 9, 2025, 3:17 a.m.