Forgot to commit RAW reader function

R/leMsmsRaw.R

@@ -380,9 +380,9 @@ findMsMsHRperxcms <- function(fileName, cpdID, mode="pH", findPeaksArgs = NULL,
 		
 		P <- lapply(1:length(spectra), function(i){
 			sp <- toRMB(spectra[[i]], cpdID[i], mode)
-			sp@id <- as.character(as.integer(cpdID))
-			sp@name <- findName(cpdID)
-			sp@formula <- findFormula(cpdID)
+			sp@id <- as.character(as.integer(cpdID[i]))
+			sp@name <- findName(cpdID[i])
+			sp@formula <- findFormula(cpdID[i])
 			sp@mode <- mode
 			return(sp)
 		})
@@ -436,17 +436,11 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs =
 		xrs[[1]] <- xrmsms
 	}
 	
-	# Fake s simplistic xcmsSet
+	# Fake a simplistic xcmsSet
 	suppressWarnings(setReplicate <- xcms::xcmsSet(files=fileName, method="MS1"))
 	xsmsms <- as.list(replicate(length(xrs),setReplicate))
 	
-	mzabs <- 0.1
-	
-	# Where is the wanted isolation ?
-	# precursorrange <- range(which(xrmsms@msnPrecursorMz == parentMass)) ## TODO: add ppm one day
-
-
-	
+	mzabs <- 0.1	
 
 	# Definitions
 	whichmissing <- vector()

R/msmsRead.R

@@ -304,35 +304,51 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
 			devnull <- capture.output(anmsms[[i]] <- CAMERA::xsAnnotate(xsmsms[[i]]))
 			devnull <- capture.output(anmsms[[i]] <- CAMERA::groupFWHM(anmsms[[i]]))
 
-				if(length(candidates[[i]]) > 0){
+			if(length(candidates[[i]]) > 0){
 				closestCandidate <- which.min (abs( RT - pl[candidates[[i]], "rt", drop=FALSE]))
 				psp[[i]] <- which(sapply(anmsms[[i]]@pspectra, function(x) {candidates[[i]][closestCandidate] %in% x}))
-				} else{psp[[i]] <- which.min( abs(getRT(anmsms[[i]]) - RT) )}
-				## Now find the pspec for compound       
+			} else{
+				psp[[i]] <- which.min( abs(getRT(anmsms[[i]]) - RT) )
+			}
+			## Now find the pspec for compound       
 
-				## 2nd best: Spectrum closest to MS1
-				##psp <- which.min( abs(getRT(anmsms) - actualRT))
+			## 2nd best: Spectrum closest to MS1
+			##psp <- which.min( abs(getRT(anmsms) - actualRT))
 
-				## 3rd Best: find pspec closest to RT from spreadsheet
-				##psp <- which.min( abs(getRT(anmsms) - RT) )
-				if((plots == TRUE) && (length(psp[[i]]) > 0)){
-					CAMERA::plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE,  mzrange=c(0, findMz(cpdids[1])[[3]]), maxlabel=10)
-				}
-				if(length(psp[[i]]) != 0){
-					spectra[[i]] <- CAMERA::getpspectra(anmsms[[i]], psp[[i]])
-				} else {whichmissing <- c(whichmissing,i)}
+			## 3rd Best: find pspec closest to RT from spreadsheet
+			##psp <- which.min( abs(getRT(anmsms) - RT) )
+			if((plots == TRUE) && (length(psp[[i]]) > 0)){
+				CAMERA::plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE,  mzrange=c(0, findMz(cpdids[1])[[3]]), maxlabel=10)
 			}
-		}
-		if(length(spectra) != 0){
-			for(i in whichmissing){
-				spectra[[i]] <- matrix(0,2,7)
+			if(length(psp[[i]]) != 0){
+				spectra[[i]] <- CAMERA::getpspectra(anmsms[[i]], psp[[i]])
+			} else {
+				whichmissing <- c(whichmissing,i)
 			}
 		}
-		
-	if(length(w@specs) != 0){
-		w@specs <- c(w@specs,list(toRMB(spectra,cpdids[1],mode)))
-	} else {
-		w@specs[[1]] <- toRMB(spectra,cpdids[1],mode)
+	}
+	if(length(spectra) != 0){
+		for(i in whichmissing){
+			spectra[[i]] <- matrix(0,2,7)
+		}
+	}
+	
+	sp <- toRMB(spectra,cpdids,"mH")
+	sp@id <- as.character(as.integer(cpdids))
+	sp@name <- findName(cpdids)
+	sp@formula <- findFormula(cpdids)
+	sp@mode <- mode
+
+	if(length(w@spectra) != 0){
+		IDindex <- sapply(w@spectra,function(s) s@id == cpdids)
+		if(length(IDindex)){
+			spectraNum <- length(w@spectra[[which(IDindex)]]@children)
+			w@spectra[[which(IDindex)]]@children[[spectraNum+1]] <- sp@children[[1]]
+		} else {
+			w@spectra[[length(www@spectra)+1]] <- sp
+		}
+	} else{
+		w@spectra[[1]] <- sp
 	}
 	
 	if(all(w@files != xRAW[[1]]@filepath)){
@@ -346,6 +362,7 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
 			}
 		}
 	}
-	names(w@specs)[length(w@specs)] <- basename(w@files[length(w@files)])
+	
 	return(w)
-}
\ No newline at end of file
+}
+

R/settings_example.R

@@ -3,9 +3,11 @@ NULL
 
 .checkMbSettings <- function()
 {
-  o <- getOption("RMassBank", NULL)
-  if(is.null(o))
-    stop("Please load your settings before using the RMassBank workflow.")
+	o <- getOption("RMassBank", NULL)
+	if(is.null(o)){
+		stop("Please load your settings before using the RMassBank workflow.")
+	}
+	
 }
 
 

man/checkIsotopes.Rd

@@ -4,7 +4,7 @@
 \alias{checkIsotopes}
 \title{Checks for isotopes in a \code{msmsWorkspace}}
 \usage{
-checkIsotopes(w, mode = "pH", intensity_cutoff = 5000,
+checkIsotopes(w, mode = "pH", intensity_cutoff = 1000,
   intensity_precision = "low", conflict = "dppm", isolationWindow = 4,
   evalMode = "complete", plotSpectrum = TRUE,
   settings = getOption("RMassBank"))
@@ -22,9 +22,9 @@ checkIsotopes(w, mode = "pH", intensity_cutoff = 5000,
 \item{conflict}{Either "isotopic"(Peak formulas are always chosen if they fit the requirements for an isotopic peak)
 or "strict"(Peaks are only marked as isotopic when there hasn't been a formula assigned before.)}
 
-\item{isolationWindow}{The width of the isolation window in Da}
+\item{isolationWindow}{Half of the width of the isolation window in Da}
 
-\item{evalMode}{Currently no function yet, but planned}
+\item{evalMode}{Currently no function yet, but planned. Currently must be "complete"}
 
 \item{plotSpectrum}{A boolean specifiying whether the spectrumshould be plotted}
 

man/filterMultiplicity.Rd

@@ -56,7 +56,7 @@ for further processing with \code{\link{mbWorkflow}}.
 \examples{
 \dontrun{
     refilteredRcSpecs <- filterMultiplicity(
-			reanalyzedRcSpecs, "myarchive", "pH")
+			w, "myarchive", "pH")
 }
 }
 \author{