R/cat.null.approx2.R

In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

cat.null.approx2<-function(z,n.cl,n.cat,n.interval=NULL,df.dens=NULL,knots.mode=NULL,type.nclass="wand"){
	df.chisq<-(n.cl-1)*(n.cat-1)
	p.value<-1-pchisq(z,df.chisq)
	n.z<-length(z)
	vec.pos<-length(z)*p.value
	z.null<-dchisq(z,df.chisq)
	if(is.null(df.dens))
		df.dens<-ifelse(df.chisq<=2,3,5)
	if(is.null(knots.mode))
		knots.mode<-ifelse(df.chisq<=2,FALSE,TRUE)
	z.fit<-denspr(z,n.interval=n.interval,df=df.dens,knots.mode=knots.mode,type.nclass=type.nclass)$y
	return(list(ratio=z.null/z.fit,vec.pos=vec.pos,vec.neg=numeric(n.z)))
}