library(fastJT)
simdat<-function(n,maf,p,mu){
    geno<-rbinom(n,2,maf)
    y<-rnorm(n)
    i2<-(geno==2)
    n2<-sum(i2)
    y2<-rnorm(n2,mu)
    y[i2]<-ifelse(rbinom(n2,1,p)==1,y2,y[i2])
    pvallm<-summary(lm(y~geno))$coef["geno","Pr(>|t|)"]
	pvalfastJT <- pvalues(fastJT(as.matrix(y,ncol=1), as.matrix(geno,ncol=1), outTopN=NA))
    c(pvallm, pvalfastJT)
}

res <- NULL
res1 <- NULL
res2 <- NULL
res3 <-NULL
set.seed(1234)
for(rate in (seq(1:15)*0.01)){
	cat("rate: ")
	cat(rate)
	cat("\n")
	if(is.null(res))
	{
		res <- rowMeans(replicate(10000, simdat(500,0.2, rate ,8))< 0.05)
		res1 <- rowMeans(replicate(10000, simdat(500,0.3, rate ,8))< 0.05)
		res2 <- rowMeans(replicate(10000, simdat(500,0.4, rate ,8))< 0.05)
		res3 <- rowMeans(replicate(10000, simdat(500,0.5, rate ,8))< 0.05)
	}
	else
	{
		res <- rbind(res, rowMeans(replicate(10000, simdat(500,0.2, rate ,8))< 0.05))
		res1 <- rbind(res1, rowMeans(replicate(10000, simdat(500,0.3, rate ,8))< 0.05))
		res2 <- rbind(res2, rowMeans(replicate(10000, simdat(500,0.4, rate ,8))< 0.05))
		res3 <- rbind(res3, rowMeans(replicate(10000, simdat(500,0.5, rate ,8))< 0.05))
	}
}


save(res,res1,res2,res3, file="typeIRlmVSjt.RData")