diff massdb-helper.R @ 2:20d69a062da3 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/massdb-helper.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,92 @@
+simplifySpectrum <- function(spec) {
+	if(length(spec) == 0){
+		return(NA_real_)
+	}
+	#print(spec)
+	if (nrow(spec) == 0)
+		return(NA_real_)
+	if (ncol(spec) != 2) {
+		spec[, BIODB.PEAK.MZ]
+		mint <- BIODB.GROUP.INTENSITY %in% colnames(spec)
+		pint <- which(mint[1])
+		if (length(pint) == 0)
+			stop(
+				"No intensity column founds, if there is more than 2 column, columns should be named",
+				paste0(BIODB.GROUP.INTENSITY, collapse = ", ")
+			)
+		spec <- spec[, c(BIODB.PEAK.MZ, BIODB.GROUP.INTENSITY[pint[1]])]
+		###Normalizing the intenities.
+	}
+	spec[, 2] <- as.numeric(spec[, 2]) * 100 / max(as.numeric(spec[, 2]))
+	colnames(spec) <- c(BIODB.PEAK.MZ, BIODB.PEAK.RELATIVE.INTENSITY)
+	spec
+}
+
+
+
+calcDistance <-
+	function(spec1 ,
+			 spec2,
+			 npmin = 2,
+			 fun = c("wcosine"),
+			 params = list()) {
+		#fun <- match.arg(fun)
+		
+		#SPec are always notmlized in pourcentage toa voir issues;
+		spec1 <- simplifySpectrum(spec1)
+		spec2 <- simplifySpectrum(spec2)
+		if(is.na(spec1)||is.na(spec2)) return(list(matched=numeric(0),similarity=0))
+		params$mz1 <- as.numeric(spec1[, BIODB.PEAK.MZ])
+		params$mz2 <- as.numeric(spec2[, BIODB.PEAK.MZ])
+		params$int1 <- as.numeric(spec1[, BIODB.PEAK.RELATIVE.INTENSITY])
+		params$int2 <- as.numeric(spec2[, BIODB.PEAK.RELATIVE.INTENSITY])
+		res <- do.call(fun, args = params)
+		if (sum(res$matched != -1) < npmin)
+			return(list(matched = res$matched, similarity = 0))
+		list(matched = res$matched,
+			 similarity = res$measure)
+	}
+
+
+
+###The returned sim list is not ordered
+compareSpectra <-
+	function(spec,
+			 libspec,
+			 npmin = 2,
+			 fun = BIODB.MSMS.DIST.WCOSINE,
+			 params = list(),
+			 decreasing = TRUE) {
+		#fun <- match.arg(fun)
+		if (length(libspec) == 0) {
+			return(NULL)
+		}
+		if (nrow(spec) == 0) {
+			return(NULL)
+		}
+		
+		####spec is directly normalized.
+		vall <-
+			sapply(
+				libspec,
+				calcDistance,
+				spec1 = spec,
+				params = params,
+				fun = fun,
+				simplify = FALSE
+			)
+		####the list is ordered with the chosen metric.
+		sim <-
+			vapply(vall,
+				   '[[',
+				   i = "similarity",
+				   FUN.VALUE = ifelse(decreasing, 0, 1))
+		osim <- order(sim, decreasing = decreasing)
+		matched <- sapply(vall, '[[', i = "matched", simplify = FALSE)
+		
+		return(list(
+			ord = osim,
+			matched = matched,
+			similarity = sim
+		))
+	}