#'
#' @title Generates phenotype status
#' @description Generates affected and non-affected subjects
#' @param num.obs Number of observations to generate per iteration
#' @param disease.prev Prevalence of the binary outcome
#' @param genotype Exposure data for genetic determinant
#' @param environment Exposure data for environment
#' @param interaction data
#' @param subject.effect.data Subject effect data, reflects the heterogenity
#' in baseline disease risk
#' @param geno.OR Odds ratios of the genetic determinant
#' @param env.OR Odds ratios of the two environments
#' @param int.OR Odds ration of the interaction
#' @return A dataframe of phenotype
#' @keywords internal
#' @author Gaye A.
#'
sim.pheno.bin.GxE <-
function(num.obs=NULL, disease.prev=NULL, genotype=NULL, environment=NULL, interaction=NULL,
subject.effect.data=NULL, geno.OR=NULL, env.OR=NULL, int.OR=NULL)
{
# GET THE ALPHA AND BETA VALUES
alpha <- log(disease.prev/(1-disease.prev))
geno.beta <- log(geno.OR)
env.beta <- log(env.OR)
int.beta <- log(int.OR)
# GENERATE THE LINEAR PREDICTOR
lp <- alpha + (geno.beta*genotype) + (env.beta*environment) + (int.beta*interaction) + subject.effect.data
# GET THE 'mu' THE PROBABILITY OF DISEASE THROUGH LOGISTIC TRANSFORMATION
mu <- exp(lp)/(1 + exp(lp))
# GENERATE THE PHENOTYPE DATA AND RETURN IT AS A DATAFRAME
phenotype <- rbinom(num.obs,1,mu)
return(phenotype)
}
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