R/centerprob.R

In CNprep: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events

centerprob <-
function(logr,emfit,zgroup,times,center){ 
	gz<-matrix(nrow=length(logr),ncol=length(emfit$parameters$mean),data=logr)
	#gz<-t(emfit$pro*exp(-0.5*(t(gz)-emfit$mu)^2/emfit$sigma)/
	#sqrt(2*pi*emfit$sigma))
	if(length(emfit$parameters$mean)==1)epro<-as.vector(1)
	if(length(emfit$parameters$mean)>1)epro<-emfit$parameters$pro        
	gz<-t(epro*pnorm(-abs(t(gz)-emfit$parameters$mean)/
		sqrt(emfit$parameters$variance$sigmasq)))        
	gz<-gz%*%t(zgroup) # combine columns of z table using indicator matrix zgroup 
	gz<-matrix(ncol=ncol(gz),
		data=apply(gz,2,cumsum)[seq(from=times,to=nrow(gz),by=times),]/times)
	#mean value within each segment
	gz<-(gz[,center]-c(0,gz[-nrow(gz),center]))/sum(epro[zgroup[center,]==1]) 
	return(ifelse(gz<0.5,gz,1-gz))
}