R/simCNVdataBinary.R

In CNVassoc: Association Analysis of CNV Data and Imputed SNPs

simCNVdataBinary<-function(n, mu.surrog, sd.surrog, w, p0, or, cnv.random=FALSE){
  k<-length(w)
  if (cnv.random){
    nj <- rmultinom(n = 1, size = n, prob = w)
  }else{
    nj <- round(n*w)
    nj[1] <- nj[1]+n-sum(nj)
  }
  surrog<-unlist(sapply(seq(along = nj), function(j) rnorm(nj[j], mean = mu.surrog[j], sd = sd.surrog[j])))
  cnv<-rep(1:k,nj)
  p<-rep(NA,k)
  p[1]<-p0
  for (j in 2:k) p[j]<-p[1]*or[j-1]/(1+p[1]*(or[j-1]-1))
  resp<-unlist(sapply(1:k,function(j) rbinom(nj[j],1,p[j]),simplify=FALSE))
  out<-data.frame(resp,cnv,surrog)
  out<-out[sample(1:n),]
  out
}