R/isPeak.R

In PROcess: Ciphergen SELDI-TOF Processing

isPeak <- function(f,SoN=2,span=81, sm.span=11,
	plot=FALSE, add=FALSE, zerothrsh=2, area.w=0.003,
	ratio=.2, ...){

	parea <- function(f, pt, eps=area.w) {
        	x <- f[,1]
        	sum(f[x <=pt*(1+eps) & x>=pt*(1-eps),2])
	} # area within .3% of peak

        n <- dim(f)[1]
	mz <- f[,1]
        lo <- lnn(f[,2], span=span, sm.span=sm.span)

        sm <- lo$fitted

        ispeak <- peaks(sm, span)

        sigmas <- lo$s

        peak <- ispeak &  sm > zerothrsh & sm > SoN * sigmas

	area <- sapply(mz[peak], parea, f=cbind(mz,sm)[!peak,])
	As <- rep(NA, length(peak))
	As[peak] <- area
	
	peak[peak] <- peak[peak] & area/ max(area) > ratio

	pks <- data.frame(peak=peak, smooth=sm, mz=mz, 
		sigmas=sigmas, area=As)
	
        if (plot) {
	  if (add) {
		lines(mz, sm, col="cyan")
		points(mz[peak],sm[peak], col="orange")
	  } else specZoom(pks, ...)
        }
	return(pks)
}