annotate spec-dist.R @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

#dyn.load('src/closeMatchPpm.dll')
# commented out for refactoring as package
#dyn.load('src/closeMatchPpm.so')

matchPpm <- function(x, y, ppm = 3, mzmin = 0) {
	if (any(is.na(y)))
		stop("NA's are not allowed in y !\n")
	ok <- !(is.na(x))
	ans <- order(x)
	keep <- seq_along(ok)[ok]
	xidx <- ans[ans %in% keep]
	xs <- x[xidx]
	yidx <- order(y)
	ys <- y[yidx]
	if (!is.double(xs))
		xs <- as.double(xs)
	if (!is.double(ys))
		ys <- as.double(ys)
	if (!is.integer(xidx))
		xidx <- as.integer(xidx)
	if (!is.integer(yidx))
		yidx <- as.integer(yidx)
	
	fm <-
		.Call(
			"closeMatchPpm",
			xs,
			ys,
			xidx,
			yidx,
			as.integer(length(x)),
			as.double(ppm),
			as.double(mzmin)
		)
	fm
}


simpList <- function(v) {
	vapply(v, function(x) {
		if (is.null(x)) {
			-1
		} else{
			x
		}
	}, FUN.VALUE = -1)
}


##Stein and scott values : mzexp 3 intexp 0.6
##Massbank values : mzexp 2 intexp 0.5


cosine <-
	function(mz1,
			 mz2,
			 int1,
			 int2,
			 mzexp = 2,
			 intexp = 0.5,
			 ppm,
			 dmz = 0.005) {
		matchList <- matchPpm(mz1, mz2, ppm, dmz)
		###Weigthed intensity
		pfound <- which(!sapply(matchList, is.null, simplify = TRUE))
		
		###If no peak is found.
		if (length(pfound) == 0)
			return(list(measure = 0, matched = rep(-1, length(mz1))))
		w1 <- int1 ^ intexp * mz1 ^ mzexp
		w2 <- int2 ^ intexp * mz2 ^ mzexp
		cat(w1[pfound], w2[unlist(matchList[pfound])],'\n')
		cos_value <-
			sum((w1[pfound] * w2[unlist(matchList[pfound])]) ^ 2) / (sum(w1[pfound] ^
																		 	2) * sum(w2[unlist(matchList[pfound])] ^ 2))
		
		####Adding the penality if needed.
		list(measure = cos_value, matched = simpList(matchList))
	}


###penalized cosine

wcosine <-
	function(mz1,
			 mz2,
			 int1,
			 int2,
			 mzexp = 2,
			 intexp = 0.5,
			 ppm,
			 dmz = 0.005,
			 penality = c("rweigth")) {
		penality <- match.arg(penality)
		matchList <- matchPpm(mz1, mz2, ppm, dmz)
		###Weigthed intensity
		pfound <- which(!sapply(matchList, is.null, simplify = TRUE))
		###If no peak is found.
		if (length(pfound) == 0)
			return(list(measure = 0, matched = rep(-1, length(mz1))))
		w1 <- int1 ^ intexp * mz1 ^ mzexp
		w2 <- int2 ^ intexp * mz2 ^ mzexp
		
		cos_value <-
			sum((w1[pfound] * w2[unlist(matchList[pfound])]) ^ 2) / (sum(w1[pfound] ^
																		 	2) * sum(w2[unlist(matchList[pfound])] ^ 2))
		
		if(is.nan(cos_value)) cos_value <- 0
		####Adding the penality if needed.
		div = 1
		if (penality == "rweigth") {
			p <-
				(sum(w1[pfound]) / sum(w1) + sum(w2[unlist(matchList[pfound])]) / sum(w2)) /
				2
			div = 2
		} else{
			p <- 0
		}
		
		measure <-  (cos_value + p) / div
		if(is.nan(measure)) measure <-  (cos_value) / div
		list(measure = measure,
			 matched = simpList(matchList))
	}

##A gaussian of the two spectra seen as a mixture of gaussian, derived form Heinonen et al 2012
pkernel <-
	function(mz1,
			 mz2,
			 int1,
			 int2,
			 mzexp = 2,
			 intexp = 0.5,
			 ppm,
			 dmz = 0.005,
			 sigint = 0.5,
			 penality = c("rweigth")) {
		###We first match the peak
		matchList <- matchPpm(mz1, mz2, ppm, dmz)
		# ###Weigthed intensity
		pfound <- which(!sapply(matchList, is.null, simplify = TRUE))
		#
		###If no peak is found.
		if (length(pfound) == 0)
			return(list(measure = 0, matched = rep(-1, length(mz1))))
		w1 <- int1 ^ intexp * mz1 ^ mzexp
		w2 <- int2 ^ intexp * mz2 ^ mzexp
		w1 <- w1 * 1 / sum(w1)
		w2 <- w2 * 1 / sum(w2)
		l1 <- length(w1)
		l2 <- length(w2)
		###The mz dev
		vsig1 = mz1 * ppm * 3 * 10 ^ -6
		vsig1 = sapply(vsig1, function(x, y) {
			return(max(x, y))
		}, y = dmz)
		
		vsig2 = mz2 * ppm * 3 * 10 ^ -6
		vsig2 = sapply(vsig2, function(x, y) {
			return(max(x, y))
		}, y = dmz)
		accu = 0
		###TO DO rcopder en C
		for (i in 1:l1) {
			for (j in 1:l2) {
				divisor = max(stats::dnorm(
					mz1[i],
					mean = mz1[i],
					sd = sqrt(vsig1[i] ^ 2 + vsig1[i] ^ 2)
				),
				stats::dnorm(
					mz2[j],
					mean = mz2[j],
					sd = sqrt(vsig2[j] ^ 2 + vsig2[j] ^ 2)
				))
				if (divisor == 0)
					next
				scalet = stats::dnorm(mz1[i],
							   mean = mz2[j],
							   sd = sqrt(vsig1[i] ^ 2 + vsig2[j] ^ 2))
				accu = accu + scalet / divisor
			}
		}
		div = 1
		if (penality == "rweigth") {
			p <-
				(sum(w1[pfound]) / sum(w1) + sum(w2[unlist(matchList[pfound])]) / sum(w2)) /
				2
			div = 2
		} else{
			p <- 0
		}
		accu = accu / (l2 * l1)
		list(measure = (accu + p) / div,
			 matched = simpList(matchList))
	}