RMassBank now fully functional

R/createMassBank.R

@@ -383,6 +383,7 @@ gatherData <- function(id)
   {
     # Split the "InChiKey=" part off the key
     inchikey_split <- strsplit(inchikey, "=", fixed=TRUE)[[1]][[2]]
+	print(inchikey_split)
     # Actually retrieve data from CTS (see the webaccess scripts)
     infos <- getCtsRecord(inchikey_split)
     # Check if the name was found. If yes, OK. Otherwise, search again using
@@ -451,7 +452,7 @@ gatherData <- function(id)
   
   
   # Eliminate duplicate names from our list of 3
-  names <- as.list(unique(c(topNameN, storedName, iupacName)))
+  names <- as.list(unique(c(dbname, storedName, iupacName)))
   
   
   # Start to fill the MassBank record.
@@ -477,6 +478,7 @@ gatherData <- function(id)
   mbdata[["COMMENT"]][["ID"]] = id
   # here compound info starts
   mbdata[['CH$NAME']] <- names
+  print(mbdata[['CH$NAME']])
   # Currently we use a fixed value for Compound Class, since there is no useful
   # convention of what should go there and what shouldn't, and the field is not used
   # in search queries.
@@ -503,7 +505,7 @@ gatherData <- function(id)
   
   mbdata[['AC$INSTRUMENT']] <- getOption("RMassBank")$annotations$instrument
   mbdata[['AC$INSTRUMENT_TYPE']] <- getOption("RMassBank")$annotations$instrument_type
-	print(mbdata)
+  print(mbdata)
   return(mbdata)  
 } # function gather.mbdata
 

R/leMsMs.r

@@ -105,7 +105,7 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
 	
 	if(readMethod == "xcms"){
 		splitfn <- strsplit(w@files,'_')
-		cpdIDs <- sapply(splitfn, function(splitted){as.numeric(return(splitted[2]))})
+		cpdIDs <- sapply(splitfn, function(splitted){as.numeric(return(splitted[length(splitted)-1]))})
 		files <- list()
 		wfiles <- vector()
 			for(i in 1:length(unique(cpdIDs))) {
@@ -175,7 +175,7 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
   if(3 %in% steps)
   {
 	message("msmsWorkflow: Step 3. Aggregate all spectra")
-    w@aggregatedSpecs <- aggregateSpectra(w@analyzedSpecs)
+    w@aggregatedSpecs <- aggregateSpectra(w@analyzedSpecs, addIncomplete=TRUE)
   }
   # Step 4: recalibrate all m/z values in raw spectra
   if(4 %in% steps)

R/leMsmsRaw.R

@@ -223,7 +223,7 @@ findMsMsHR.direct <- function(msRaw, cpdID, mode = "pH", confirmMode = 0, useRtL
 #'      psp <- findMsMsHRperxcms.direct(fileList,2184)
 #' }
 #' @export
-findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs, plots = FALSE) {
+findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs = NULL, plots = FALSE) {
 	
 	require(CAMERA)
 	require(xcms)
@@ -244,7 +244,7 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs,
 	## MSMS
 	##
 	xrmsms <- xcmsRaw(fileName, includeMSn=TRUE)
-
+	print("File read")
 	## Where is the wanted isolation ?
 	precursorrange <- range(which(xrmsms@msnPrecursorMz == parentMass)) ## TODO: add ppm one day
 
@@ -259,6 +259,7 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs,
 	anmsms <- list()
 	psp <- list()
 	spectra <- list()
+	whichmissing <- vector()
 	
 	for(i in 1:length(xrs)){
 		peaks(xsmsms[[i]]) <- do.call(findPeaks,c(findPeaksArgs, object = xrs[[i]]))
@@ -283,7 +284,14 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs,
 		if((plots == TRUE) && (length(psp[[i]]) > 0)){
 			plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE,  mzrange=c(0, findMz(cpdID)[[3]]), maxlabel=10)
 		}
+		if(length(psp[[i]]) != 0){
 		spectra[[i]] <- getpspectra(anmsms[[i]], psp[[i]])
+		} else {whichmissing <- c(whichmissing,i)}
+	}
+	if(length(spectra) != 0){
+		for(i in whichmissing){
+			spectra[[i]] <- matrix(0,2,7)
+		}
 	}
 	return(spectra)
 }
@@ -413,7 +421,7 @@ toRMB <- function(msmsXCMSspecs = NA, cpdID = NA, mode="pH", MS1spec = NA){
 		header[12] <- max(spec[,1]) 
 		header[13] <- 1
 		header[14] <- findMz(cpdID)[[3]]
-		header[15] <- -1 ##Will be changed for different charges
+		header[15] <- 1 ##Will be changed for different charges
 		header[16] <- 0 ##There sadly isnt any precursor intensity to find in the msms-scans. Workaround? msmsXCMS@files[1]
 		header[17:20] <- 0 ##Will be changed if merge is wanted
 		return(header)

R/webAccess.R

@@ -138,26 +138,26 @@ getCtsRecord <- function(key, from = "inchikey",
   to = c("cas","hmdb","kegg","sid","chebi","inchi","lipidmap","smiles","cid",
          "inchikey","mass","formula","iupac","names"))
 {
-	require(devtools)
+	#require(devtools)
 	require(RJSONIO)
 	#install_github(repo = "CTSgetR", username = "dgrapov")
-	require(CTSgetR)
+	#require(CTSgetR)
 	# checks
-	if(from %in% c("", "None", "Unknown", "Not available"))
-    return(NA)
+	if(from %in% c("", "None", "Unknown", "Not available")){
+    return(NA)}
 	
-	ChemSpID<-CTSgetR(key,from="InChIKey",to="ChemSpider",parallel=FALSE)
-	CTS.options<-CTS.options()[2:10]
-	CTS.options # see options
-	id<-ChemSpID
-	childrenProc<-sapply(1:length(CTS.options), function(i)
-	{
-		cat(CTS.options[i],"\n")
-		CTSgetR(id=id,to=CTS.options[i],from="ChemSpider")
-	})
-	print(childrenProc)
+	#ChemSpID<-CTSgetR(key,from="InChIKey",to="ChemSpider",parallel=FALSE)
+	#CTS.options<-CTS.options()[2:10]
+	#CTS.options # see options
+	#id<-ChemSpID
+	#childrenProc<-sapply(1:length(CTS.options), function(i)
+	#{
+	#	cat(CTS.options[i],"\n")
+	#	CTSgetR(id=id,to=CTS.options[i],from="ChemSpider")
+	#})
+	#print(childrenProc)
 	
-	require(RJSON)
+	#require(RJSON)
 	urlInchi <- paste("http://cts.fiehnlab.ucdavis.edu/service/compound/", key, sep='')
 	JSONstring <- getURL(urlInchi)
 	Content <- fromJSON(JSONstring, method = "C", unexpected.escape = "error" )
@@ -195,10 +195,10 @@ getCtsRecord <- function(key, from = "inchikey",
   #}
 
   # Check and fix CAS (eliminate the 12-34-5CHEBI and NIKKAJI stuff)
-  if(!is.null(childrenProc$CAS))
-  {
-    childrenProc$CAS <- childrenProc$CAS[which(grepl("^[-0-9]+$", childrenProc$CAS))]
-  }
+  #if(!is.null(childrenProc$CAS))
+  #{
+    #childrenProc$CAS <- childrenProc$CAS[which(grepl("^[-0-9]+$", childrenProc$CAS))]
+  #}
   print(Content)
   return(Content)
 }
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