R/getRidgeValue.R

In MassSpecWavelet: Mass spectrum processing by wavelet-based algorithms

"getRidgeValue" <-
function(ridgeList, wCoefs, skip=0) {
	
	ridgeLen <- sapply(ridgeList, length)
	ridgeName <- names(ridgeList)
	ridgeInfo <- matrix(as.numeric(unlist(strsplit(ridgeName, '_'))), nrow=2)
	ridgeLevel <- ridgeInfo[1,]
	mzInd <- ridgeInfo[2,]
	
	scales <- attr(ridgeList, 'scales')
	if (is.null(scales)) scales <- 0:max(ridgeLen)
	if (length(scales) != ncol(wCoefs))  stop('The length of "scales" does not match with "wCoefs"!')
	skip <- as.character(skip)
	
	ridgeValue <- NULL
	ridgeMax <- NULL
	for (i in 1:length(mzInd)) {
		ridge.i <- ridgeList[[i]]
		level.i <- ridgeLevel[i]
		levels.i <- level.i:(level.i + ridgeLen[i] - 1)
		scales.i <- scales[levels.i]
		removeInd.i <- which(scales.i == skip)
		if (length(removeInd.i) > 0) {
			levels.i <- levels.i[-removeInd.i]
			ridge.i <- ridge.i[-removeInd.i]
			scales.i <- scales.i[-removeInd.i]		
		}
		coefInd.i <- cbind(ridge.i, levels.i)
		ridgeValue.i <- wCoefs[coefInd.i]
		names(ridgeValue.i) <- scales.i
		ridgeValue <- c(ridgeValue, list(ridgeValue.i))
		ridgeMax <- c(ridgeMax, max(ridgeValue.i))
	}
	names(ridgeValue) <- names(ridgeMax) <- ridgeName
	attr(ridgeValue, 'ridgeMax') <- ridgeMax
	return(ridgeValue)
}