diff --git a/DESCRIPTION b/DESCRIPTION
index 5e4961f976d57082891aa25b18f0bb9a3515b702..ef8ba0abeb2e598694ae39996b6b0ffe1b58453a 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -33,7 +33,8 @@ Suggests:
xcms (>= 1.37.1),
CAMERA,
ontoCAT,
- RUnit
+ RUnit,
+ enviPat
Collate:
'alternateAnalyze.R'
'createMassBank.R'
diff --git a/R/Isotopic_Annotation.R b/R/Isotopic_Annotation.R
index 8d08545b154588940dabc439e64c50b7bfa7b90f..be74a552ec2125db042bf4a000a854dcc57a1b91 100644
--- a/R/Isotopic_Annotation.R
+++ b/R/Isotopic_Annotation.R
@@ -29,9 +29,9 @@ checkIsotopes <- function(w, mode = "pH", intensity_cutoff = 5000, intensity_pre
isolationWindow = 4, evalMode = "complete", plotSpectrum = TRUE, settings = getOption("RMassBank")){
# Load library and data
- require(enviPat)
- data("isotopes")
+ requireNamespace("enviPat",quietly=TRUE)
+ data("isotopes", package="enviPat")
if(!(intensity_precision %in% c("none","low","high"))){
stop('intensity_precision must be specified as either "none", "low" or "high"')
@@ -116,11 +116,14 @@ checkIsotopes <- function(w, mode = "pH", intensity_cutoff = 5000, intensity_pre
# Find parent formula and cpdID
parent_formula <- add.formula(spec@formula, allowed_additions)
id <- as.numeric(spec@id)
-
+ specNum <- 0
+ specEnv <- environment()
# lapply over all extracted MS2 spectra
lapply(spec@children, function(msmsdata){
+ specEnv$specNum <- specEnv$specNum + 1
+
# Extract currently relevant peaks
currentMPeaks <- matchedPeaks[(matchedPeaks$cpdID == id) & (matchedPeaks$scan == msmsdata@acquisitionNum),,drop=FALSE]
currentUPeaks <- unmatchedPeaks[(unmatchedPeaks$cpdID == id) & (unmatchedPeaks$scan == msmsdata@acquisitionNum),,drop=FALSE]
@@ -132,7 +135,7 @@ checkIsotopes <- function(w, mode = "pH", intensity_cutoff = 5000, intensity_pre
# Sort pattern by abundance
isoMPatterns <- lapply(currentMPeaks$formula, function(formula){
# Find pattern
- pattern <- as.data.frame(isopattern(formula, isotopes = isotopes)[[1]])
+ pattern <- as.data.frame(enviPat::isopattern(formula, isotopes = isotopes)[[1]])
mass <- findMz.formula(formula,"")$mzCenter
# Find index of nonisotopic molecule and
@@ -221,6 +224,14 @@ checkIsotopes <- function(w, mode = "pH", intensity_cutoff = 5000, intensity_pre
# Which isotope patterns still have theoretical intensities above the cutoff?
peaksToCheck <- which(as.logical(sapply(isoMPatterns,nrow)))
+ if(!length(peaksToCheck)){
+ warning(paste0("The peaks of compound ", id, " in spectrum #", specEnv$specNum," are not intense enough to search for isotopic peaks"))
+ if(plotSpectrum){
+ plot(currentMPeaks$mzFound, currentMPeaks$intensity,type="h", main=paste(id,findName(id)), col="black", xlab="m/z", ylab="intensity", lwd=3)
+ }
+ return(0)
+ }
+
# Now, look for isotopic patterns in unmatched peaks with all specified parameters
if("add" %in% evalMode){
# Which peaks have no correct formula annotation as of now?
@@ -384,10 +395,11 @@ checkIsotopes <- function(w, mode = "pH", intensity_cutoff = 5000, intensity_pre
}
if(nrow(correctionMatrix)){
points(correctionMatrix$mzFound, correctionMatrix$intensity,type="h", col="yellow", lwd=3)
+ if(nrow(conflictedMatrix)){
+ points(conflictedMatrix$mzFound, conflictedMatrix$intensity,type="h", col="red", lwd=3)
+ }
}
- if(nrow(conflictedMatrix)){
- points(conflictedMatrix$mzFound, conflictedMatrix$intensity,type="h", col="red", lwd=3)
- }
+
}
}
return(0)
diff --git a/R/RmbWorkspace.R b/R/RmbWorkspace.R
index 69fd5dbab8fb4f0ca4ccbdc3d561056bd7ad8952..91d73b9a8f5c51bfb3d5efe4924fe121e0ceaa41 100755
--- a/R/RmbWorkspace.R
+++ b/R/RmbWorkspace.R
@@ -354,14 +354,7 @@ setMethod("show", "msmsWorkspace",
## msmsWorkflow: Step 4. Recalibrate m/z values in raw spectra
if(4 %in% progress){
- cat("Peaks found after Step 4:\n")
- dummy <- sapply(object@spectra, function(x) cat(" -", x@id, "\t found:", x@found, "\n"))
- cat("Peaks found:\n")
- dummy4 <- sapply(object@spectra, function(x){
- cat(" -", x@id, "\t peaks:",
- sapply(x@children, function(s) s@peaksCount), "\n")
- return(sapply(x@children, function(s) s@peaksCount))
- })
+ cat("Peaks successfully recalibrated:\n")
}
## msmsWorkflow: Step 5. Reanalyze recalibrated spectra
diff --git a/R/alternateAnalyze.R b/R/alternateAnalyze.R
index 98f8856f2f168cc106a78bb665946c733df2636e..fd11ab752c3192d7da878a006d5344432ced007a 100644
--- a/R/alternateAnalyze.R
+++ b/R/alternateAnalyze.R
@@ -83,14 +83,11 @@ analyzeMsMs.optimized <- function(msmsPeaks, mode="pH", detail=FALSE, run="preli
if(method=="formula")
{
return(analyzeMsMs.formula.optimized(msmsPeaks, mode, detail, run, filterSettings,
- spectraList, fragData, fragDataIndex
- ))
+ spectraList, fragData, fragDataIndex))
}
else if(method == "intensity")
{
- return(analyzeMsMs.intensity(msmsPeaks, mode, detail, run, filterSettings,
- spectraList
- ))
+ return(analyzeMsMs.intensity(msmsPeaks, mode, detail, run, filterSettings))
}
}
diff --git a/R/leMsMs.r b/R/leMsMs.r
index 5dc5b5bbe71ad51760696565217533b809b36d04..6d2d850a66be9b6ae8444a6d286e94002f1f3d4e 100755
--- a/R/leMsMs.r
+++ b/R/leMsMs.r
@@ -1145,6 +1145,7 @@ processProblematicPeaks <- function(w, mode, archivename = NA)
,,drop=FALSE], peaksMatched(w), mode)
fp$OK <- rep('', nrow(fp))
fp$name <- rownames(fp)
+
fp <- fp[with(fp,
order(cpdID, mzCalc, scan)),
]
@@ -1367,10 +1368,10 @@ plotRecalibration.direct <- function(rcdata, rc, rc.ms1, title, mzrange,
if((length(unique(rcdata$mzFound))>1) &
(length(unique(rcdata$recalfield))>1))
{
- if(require(gplots))
+ if(requireNamespace("gplots",quietly=TRUE))
{
- hist2d(rcdata$mzFound, rcdata$recalfield,
+ gplots::hist2d(rcdata$mzFound, rcdata$recalfield,
col=c("white", heat.colors(12)), xlab="m/z",
ylab = ylab.plot, main=paste(title, "density"))
lines(RcModelMz, RcModelRecal, col="blue")
diff --git a/R/leMsmsRaw.R b/R/leMsmsRaw.R
index 54b6f56179c951630cb90137c1f2c0c389527e3a..ca7dee120f2b9144cf154fd249146f24af336190 100644
--- a/R/leMsmsRaw.R
+++ b/R/leMsmsRaw.R
@@ -359,12 +359,12 @@ findMsMsHR.direct <- function(msRaw, cpdID, mode = "pH", confirmMode = 0, useRtL
#' @export
findMsMsHRperxcms <- function(fileName, cpdID, mode="pH", findPeaksArgs = NULL, plots = FALSE, MSe = FALSE){
-
-
+ # Find mz
mzLimits <- findMz(cpdID, mode)
mz <- mzLimits$mzCenter
-
+
+ # If there are more files than cpdIDs
if(length(fileName) > 1){
fspectra <- list()
@@ -374,7 +374,8 @@ findMsMsHRperxcms <- function(fileName, cpdID, mode="pH", findPeaksArgs = NULL,
spectra <- toRMB(unlist(unlist(fspectra, FALSE),FALSE), cpdID, mode)
- } else if(length(cpdID) > 1){
+ } else if(length(cpdID) > 1){ # If there are more cpdIDs than files
+
spectra <- findMsMsHRperxcms.direct(fileName, cpdID, mode=mode, findPeaksArgs = findPeaksArgs, plots = plots, MSe = MSe)
P <- lapply(1:length(spectra), function(i){
@@ -387,7 +388,7 @@ findMsMsHRperxcms <- function(fileName, cpdID, mode="pH", findPeaksArgs = NULL,
})
return(P)
- } else {
+ } else { # There is a file for every cpdID
spectra <- toRMB(unlist(findMsMsHRperxcms.direct(fileName, cpdID, mode=mode, findPeaksArgs = NULL, plots = FALSE, MSe = FALSE),FALSE))
}
@@ -406,15 +407,15 @@ findMsMsHRperxcms <- function(fileName, cpdID, mode="pH", findPeaksArgs = NULL,
#' @export
findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs = NULL, plots = FALSE, MSe = FALSE) {
- require(CAMERA)
- require(xcms)
+ requireNamespace("CAMERA",quietly=TRUE)
+ requireNamespace("xcms",quietly=TRUE)
##
## getRT function
##
getRT <- function(xa) {
- rt <- sapply(xa@pspectra, function(x) {median(peaks(xa@xcmsSet)[x, "rt"])})
+ rt <- sapply(xa@pspectra, function(x) {median(xcms::peaks(xa@xcmsSet)[x, "rt"])})
}
##
@@ -422,13 +423,13 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs =
##
# Read file
- suppressWarnings(xrmsms <- xcmsRaw(fileName, includeMSn=TRUE))
+ suppressWarnings(xrmsms <- xcms::xcmsRaw(fileName, includeMSn=TRUE))
# If file is not MSe, split by collision energy
if(MSe == FALSE){
# Also, fake MS1 from the MSn data
- suppressWarnings(xrs <- split(msn2xcmsRaw(xrmsms), f = xrmsms@msnCollisionEnergy))
+ suppressWarnings(xrs <- split(xcms::msn2xcmsRaw(xrmsms), f = xrmsms@msnCollisionEnergy))
} else{
# Else, MSn data will already be in MS1
xrs <- list()
@@ -436,7 +437,7 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs =
}
# Fake s simplistic xcmsSet
- suppressWarnings(setReplicate <- xcmsSet(files=fileName, method="MS1"))
+ suppressWarnings(setReplicate <- xcms::xcmsSet(files=fileName, method="MS1"))
xsmsms <- as.list(replicate(length(xrs),setReplicate))
mzabs <- 0.1
@@ -470,23 +471,23 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs =
# Go over every collision energy of the MS2
for(i in 1:length(xrs)){
- suppressWarnings(capture.output(peaks(xsmsms[[i]]) <- do.call(findPeaks,c(findPeaksArgs, object = xrs[[i]]))))
+ suppressWarnings(capture.output(xcms::peaks(xsmsms[[i]]) <- do.call(xcms::findPeaks,c(findPeaksArgs, object = xrs[[i]]))))
- if (nrow(peaks(xsmsms[[i]])) == 0) {
+ if (nrow(xcms::peaks(xsmsms[[i]])) == 0) {
XCMSspectra[[i]] <- matrix(0,2,7)
next
} else{
# Get the peaklist
- pl <- peaks(xsmsms[[i]])[,c("mz", "rt"), drop=FALSE]
+ pl <- xcms::peaks(xsmsms[[i]])[,c("mz", "rt"), drop=FALSE]
# Find precursor peak within limits
candidates <- which( pl[,"mz", drop=FALSE] < parentMass + mzabs & pl[,"mz", drop=FALSE] > parentMass - mzabs
& pl[,"rt", drop=FALSE] < RT * 1.1 & pl[,"rt", drop=FALSE] > RT * 0.9 )
# Annotate and group by FWHM (full width at half maximum)
- capture.output(anmsms <- xsAnnotate(xsmsms[[i]]))
- capture.output(anmsms <- groupFWHM(anmsms))
+ capture.output(anmsms <- CAMERA::xsAnnotate(xsmsms[[i]]))
+ capture.output(anmsms <- CAMERA::groupFWHM(anmsms))
# If a candidate fulfills the condition, choose the closest and retrieve the index of those pesudospectra
if(length(candidates) > 0){
@@ -502,12 +503,12 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs =
# If the plot parameter was supplied, plot it
if((plots == TRUE) && (length(pspIndex) > 0)){
- plotPsSpectrum(anmsms, pspIndex, log=TRUE, mzrange=c(0, findMz(cpdID)[[3]]), maxlabel=10)
+ CAMERA::plotPsSpectrum(anmsms, pspIndex, log=TRUE, mzrange=c(0, findMz(cpdID)[[3]]), maxlabel=10)
}
# If there is a number of indexes, retrieve the pseudospectra
if(length(pspIndex) != 0){
- XCMSspectra[[i]] <- getpspectra(anmsms, pspIndex)
+ XCMSspectra[[i]] <- CAMERA::getpspectra(anmsms, pspIndex)
} else {
# Else note the spectrum as missing
whichmissing <- c(whichmissing,i)
@@ -695,7 +696,7 @@ toRMB <- function(msmsXCMSspecs = NA, cpdID = NA, mode="pH", MS1spec = NA){
mz = pks[,"mz"],
intensity = pks[,"int"],
precScanNum = as.integer(1),
- precursorMz = findMz(cpdID)[[3]],
+ precursorMz = findMz(cpdID)$mzCenter,
precursorIntensity = 0,
precursorCharge = as.integer(1),
collisionEnergy = 0,
@@ -707,14 +708,7 @@ toRMB <- function(msmsXCMSspecs = NA, cpdID = NA, mode="pH", MS1spec = NA){
))
})
- msmsSpecs <- as(do.call(c, msmsSpecs), "SimpleList")
-
- parentPeak <- matrix(nrow = 1, ncol = 2)
- colnames(parentPeak) <- c("mz","int")
- parentPeak[1,] <- c(findMz(cpdID,mode=mode)$mzCenter,100)
-
-
-
+ msmsSpecs <- as(do.call(c, msmsSpecs), "SimpleList")
##Build the new objects
masterSpec <- new("Spectrum1",
@@ -761,78 +755,71 @@ toRMB <- function(msmsXCMSspecs = NA, cpdID = NA, mode="pH", MS1spec = NA){
#' addPeaksManually(w, cpdID, handSpec)
#' }
#' @export
-addPeaksManually <- function(w, cpdID, handSpec, mode = "pH"){
-
- ##Where do the peaks and the header need to be added?
- pos <- sapply(w@specs,function(spec){cpdID == spec$id})
- if(length(pos) == 0) pos <- FALSE
-
- childHeader <- matrix(0,1,20)
- childHeader[,4] <- length(handSpec[,1])
- childHeader[,5] <- 0
- childHeader[,6] <- findRt(cpdID)$RT * 60
- childHeader[,7] <- handSpec[which.max(handSpec[,"int"]),1]
- childHeader[,8] <- max(handSpec)
- childHeader[,10] <- 0
- childHeader[,11] <- min(handSpec[,"mz"])
- childHeader[,12] <- max(handSpec[,"mz"])
- childHeader[,13] <- 1
- childHeader[,14] <- findMz(cpdID)[[3]]
- childHeader[,15] <- 1 ##Will be changed for different charges
- childHeader[,16] <- 0 ##There sadly isn't any precursor intensity to find in the msms-scans. Workaround?
- childHeader[,17:20] <- 0 ##Will be changed if merge is wanted
- colnames(childHeader) <- c("seqNum", "acquisitionNum", "msLevel", "peaksCount", "totIonCurrent", "retentionTime", "basepeakMZ",
- "basePeakIntensity", "collisionEnergy", "ionisationEnergy", "lowMZ", "highMZ", "precursorScanNum",
- "precursorMZ", "precursorCharge", "precursorIntensity", "mergedScan", "mergedResultScanNum",
- "mergedResultStartScanNum", "mergedResultEndScanNum")
-
- ##If the compound for the cpdID isn't in specs yet, add a new spectrum
- if(length(which(pos)) == 0){
- pos <- length(w@specs) + 1
- childHeader[,1:3] <- 2
- w@specs[[pos]] <- list()
- w@specs[[pos]]$foundOK <- 1
- w@specs[[pos]]$parentscan <- 1
- w@specs[[pos]]$parentHeader <- matrix(0, ncol = 20, nrow = 1)
- rownames(w@specs[[pos]]$parentHeader) <- 1
- colnames(w@specs[[pos]]$parentHeader) <- c("seqNum", "acquisitionNum", "msLevel", "peaksCount", "totIonCurrent", "retentionTime", "basepeakMZ",
- "basePeakIntensity", "collisionEnergy", "ionisationEnergy", "lowMZ", "highMZ", "precursorScanNum",
- "precursorMZ", "precursorCharge", "precursorIntensity", "mergedScan", "mergedResultScanNum",
- "mergedResultStartScanNum", "mergedResultEndScanNum")
- w@specs[[pos]]$parentHeader[1,1:3] <- 1
- w@specs[[pos]]$parentHeader[1,4:20] <- 0
- w@specs[[pos]]$parentHeader[1,6] <- findRt(cpdID)$RT * 60
- w@specs[[pos]]$parentHeader <- as.data.frame(w@specs[[pos]]$parentHeader)
- w@specs[[pos]]$childScans <- 2
- w@specs[[pos]]$childHeaders <- as.data.frame(childHeader)
- w@specs[[pos]]$parentPeak <- matrix(nrow = 1, ncol = 2)
- colnames(w@specs[[pos]]$parentPeak) <- c("mz","int")
- w@specs[[pos]]$parentPeak[1,] <- c(findMz(cpdID,mode=mode)$mzCenter,100)
- w@specs[[pos]]$peaks <- list()
- w@specs[[pos]]$peaks[[1]] <- handSpec
- w@specs[[pos]]$mz <- findMz(cpdID,mode=mode)
- w@specs[[pos]]$id <- cpdID
- w@specs[[pos]]$formula <- findFormula(cpdID)
- colnames(w@specs[[pos]]$childHeaders) <- c("seqNum", "acquisitionNum", "msLevel", "peaksCount", "totIonCurrent", "retentionTime", "basepeakMZ",
- "basePeakIntensity", "collisionEnergy", "ionisationEnergy", "lowMZ", "highMZ", "precursorScanNum",
- "precursorMZ", "precursorCharge", "precursorIntensity", "mergedScan", "mergedResultScanNum",
- "mergedResultStartScanNum", "mergedResultEndScanNum")
- } else {
- pos <- which(pos)
- w@specs[[pos]]$childHeaders <- rbind(w@specs[[pos]]$childHeaders,childHeader)
- w@specs[[pos]]$childHeaders[,1] <- 2:(nrow(w@specs[[pos]]$childHeaders)+1)
- w@specs[[pos]]$childHeaders[,2] <- w@specs[[pos]]$childHeaders[,1]
- w@specs[[pos]]$childScans <- c(w@specs[[pos]]$childScans,max(w@specs[[pos]]$childScans)+1)
- w@specs[[pos]]$peaks[[length(w@specs[[pos]]$peaks)+1]] <- handSpec
- }
+addPeaksManually <- function(w, cpdID = NA, handSpec, mode = "pH"){
+
+
+ if(is.na(cpdID)){
+ stop("Please supply the compoundID!")
+ }
+
+ # For the case that the cpdID turns up for the first time
+ # a new spectrumset needs to be created
+ if(!(cpdID %in% sapply(w@spectra,function(s) s@id))){
- return(w)
+ # Create fake MS1 spectrum
+ masterSpec <- new("Spectrum1",
+ mz = findMz(cpdID,mode=mode)$mzCenter,
+ intensity = 100,
+ polarity = as.integer(0),
+ peaksCount = as.integer(1),
+ rt = findRt(cpdID)$RT,
+ acquisitionNum = as.integer(1),
+ tic = 0,
+ centroided = TRUE
+ )
+
+ # Create fake spectrumset
+ spectraSet <- new("RmbSpectraSet",
+ parent = masterSpec,
+ found = TRUE,
+ #complete = NA,
+ #empty = NA,
+ id = as.character(as.integer(cpdID)),
+ formula = findFormula(cpdID),
+ mz = findMz(cpdID,mode=mode)$mzCenter,
+ name = findName(cpdID),
+ mode = mode
+ #annotations = list()
+ )
+
+ w@spectra[[length(w@spectra) + 1]] <- spectraSet
+ }
+
+ specIndex <- which(cpdID == sapply(w@spectra, function(s) s@id))
+
+ # New spectrum object
+ w@spectra[[specIndex]]@children[[length(w@spectra[[specIndex]]@children) + 1]] <- new("RmbSpectrum2",
+ mz = handSpec[,"mz"],
+ intensity = handSpec[,"int"],
+ precScanNum = as.integer(1),
+ precursorMz = findMz(cpdID)$mzCenter,
+ precursorIntensity = 0,
+ precursorCharge = as.integer(1),
+ collisionEnergy = 0,
+ tic = 0,
+ peaksCount = nrow(handSpec),
+ rt = findRt(cpdID)$RT,
+ acquisitionNum = as.integer(length(w@spectra[[specIndex]]@children) + 2),
+ centroided = TRUE)
+ return(w)
}
+
createSpecsFromPeaklists <- function(w, cpdIDs, filenames, mode="pH"){
- for(j in 1:length(filenames)){
- w <- addPeaksManually(w,cpdIDs[j],as.matrix(read.csv(filenames[j]), header=TRUE),mode)
- }
+ for(j in 1:length(filenames)){
+ w <- addPeaksManually(w,cpdIDs[j],as.matrix(read.csv(filenames[j]), header=TRUE),mode)
+ }
+
return(w)
}
diff --git a/R/msmsRead.R b/R/msmsRead.R
index 67dac46719c932245abde4f36da07885d6e62b13..007a8cfb4ef239c16f1fad7326000394eef6460e 100644
--- a/R/msmsRead.R
+++ b/R/msmsRead.R
@@ -141,8 +141,8 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
if(readMethod == "xcms"){
##Load libraries
- require(xcms)
- require(CAMERA)
+ requireNamespace("xcms",quietly=TRUE)
+ requireNamespace("CAMERA",quietly=TRUE)
##Find unique files and cpdIDs
ufiles <- unique(w@files)
@@ -204,15 +204,6 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
}
w@files <- sapply(files,function(file){return(file[1])})
- specnames <- basename(as.character(w@files))
- if(length(unique(specnames)) == length(specnames)){
- names(w@specs) <- basename(as.character(w@files))
- } else {
- for(i in 1:length(specnames)){
- specnames[i] <- paste(i,"_",specnames[i],sep="")
- }
- }
- names(w@specs) <- specnames
message("Peaks read")
return(w)
}
@@ -251,7 +242,7 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NULL,
settings = getOption("RMassBank"), progressbar = "progressBarHook", plots = FALSE){
- require(xcms)
+ requireNamespace("xcms", quietly=TRUE)
##xRAW will be coerced into a list of length 1 if it is an xcmsRaw-object
if(class(xRAW) == "xcmsRaw"){
@@ -275,7 +266,7 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
# stop(paste("No msn data in list elements", setdiff(1:length(xRAW),msnExist)))
#}
- require(CAMERA)
+ requireNamespace("CAMERA",quietly=TRUE)
parentMass <- findMz(cpdids[1], mode=mode)$mzCenter
if(is.na(parentMass)){
@@ -289,7 +280,7 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
rt <- sapply(xa@pspectra, function(x) {median(peaks(xa@xcmsSet)[x, "rt"])})
}
- suppressWarnings(setReplicate <- xcmsSet(files=xRAW[[1]]@filepath, method="MS1"))
+ suppressWarnings(setReplicate <- xcms::xcmsSet(files=xRAW[[1]]@filepath, method="MS1"))
xsmsms <- as.list(replicate(length(xRAW),setReplicate))
candidates <- list()
anmsms <- list()
@@ -298,20 +289,20 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
whichmissing <- vector()
metaspec <- list()
for(i in 1:length(xRAW)){
- devnull <- suppressWarnings(capture.output(peaks(xsmsms[[i]]) <- do.call(findPeaks,c(findPeaksArgs, object = xRAW[[i]]))))
+ devnull <- suppressWarnings(capture.output(xcms::peaks(xsmsms[[i]]) <- do.call(xcms::findPeaks,c(findPeaksArgs, object = xRAW[[i]]))))
- if (nrow(peaks(xsmsms[[i]])) == 0) { ##If there are no peaks
+ if (nrow(xcms::peaks(xsmsms[[i]])) == 0) { ##If there are no peaks
spectra[[i]] <- matrix(0,2,7)
next
} else{
## Get pspec
- pl <- peaks(xsmsms[[i]])[,c("mz", "rt"), drop=FALSE]
+ pl <- xcms::peaks(xsmsms[[i]])[,c("mz", "rt"), drop=FALSE]
## Best: find precursor peak
candidates[[i]] <- which( pl[,"mz", drop=FALSE] < parentMass + mzabs & pl[,"mz", drop=FALSE] > parentMass - mzabs
& pl[,"rt", drop=FALSE] < RT * 1.1 & pl[,"rt", drop=FALSE] > RT * 0.9 )
- devnull <- capture.output(anmsms[[i]] <- xsAnnotate(xsmsms[[i]]))
- devnull <- capture.output(anmsms[[i]] <- groupFWHM(anmsms[[i]]))
+ devnull <- capture.output(anmsms[[i]] <- CAMERA::xsAnnotate(xsmsms[[i]]))
+ devnull <- capture.output(anmsms[[i]] <- CAMERA::groupFWHM(anmsms[[i]]))
if(length(candidates[[i]]) > 0){
closestCandidate <- which.min (abs( RT - pl[candidates[[i]], "rt", drop=FALSE]))
@@ -325,10 +316,10 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
## 3rd Best: find pspec closest to RT from spreadsheet
##psp <- which.min( abs(getRT(anmsms) - RT) )
if((plots == TRUE) && (length(psp[[i]]) > 0)){
- plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE, mzrange=c(0, findMz(cpdids[1])[[3]]), maxlabel=10)
+ CAMERA::plotPsSpectrum(anmsms[[i]], psp[[i]], log=TRUE, mzrange=c(0, findMz(cpdids[1])[[3]]), maxlabel=10)
}
if(length(psp[[i]]) != 0){
- spectra[[i]] <- getpspectra(anmsms[[i]], psp[[i]])
+ spectra[[i]] <- CAMERA::getpspectra(anmsms[[i]], psp[[i]])
} else {whichmissing <- c(whichmissing,i)}
}
}
diff --git a/R/validateMassBank.R b/R/validateMassBank.R
index 20dd4369439e28655f245323b09d0060cd0c8f06..db1bd8a3244b33fb5f05ca8ee2b0b9323f9776c4 100644
--- a/R/validateMassBank.R
+++ b/R/validateMassBank.R
@@ -19,8 +19,8 @@
#' @export
validate <- function(path, simple = TRUE) {
- require(ontoCAT)
- require(RUnit)
+ requireNamespace("ontoCAT",quietly=TRUE)
+ requireNamespace("RUnit",quietly=TRUE)
# Is the argument a directory?
# If yes, list the files
@@ -38,12 +38,12 @@ validate <- function(path, simple = TRUE) {
tests <- list()
for(i in 1:length(RMassBank.env$mb)){
if(RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS2" || RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS"){
- tests[[i]] <- defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "runit.MS2.test.R",
+ tests[[i]] <- RUnit::defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "runit.MS2.test.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
} else{
- tests[[i]] <- defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "^runit.MSn.test.[rR]$",
+ tests[[i]] <- RUnit::defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "^runit.MSn.test.[rR]$",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
@@ -51,9 +51,9 @@ validate <- function(path, simple = TRUE) {
}
print("Starting Tests")
# Testing the list of Testsuites
- testData <- suppressWarnings(runTestSuite(tests,verbose=0))
+ testData <- suppressWarnings(RUnit::runTestSuite(tests,verbose=0))
# Prints the HTML-record
- printHTMLProtocol(testData, fileName = paste0(getwd(),"/report.html"))
+ RUnit::printHTMLProtocol(testData, fileName = paste0(getwd(),"/report.html"))
if(simple){
fileConnection <- file(paste0(getwd(),"/report.html"), open = "r")
htmlFile <- readLines(fileConnection)
@@ -96,8 +96,8 @@ validate <- function(path, simple = TRUE) {
# getOntology() has a problem with reading relative Windows paths(it wants an URI),
# so the path has to be made absolute
# I reckon this should work under Linux without doing that
- ont <- getOntology(normalizePath(filename))
- if(is.null(getOntologyAccession(ont))){
+ ont <- ontoCAT::getOntology(normalizePath(filename))
+ if(is.null(ontoCAT::getOntologyAccession(ont))){
return(FALSE)
}
return(TRUE)
@@ -143,11 +143,11 @@ validate <- function(path, simple = TRUE) {
# This is a list of the possible instrument names
.getInstruments <- function(){
- Onto <- getOntology(system.file(package = "RMassBank", "psi-ms.obo"))
- instrumentTerms <- getAllTermChildrenById(Onto,"MS_1000031")
+ Onto <- ontoCAT::getOntology(system.file(package = "RMassBank", "psi-ms.obo"))
+ instrumentTerms <- ontoCAT::getAllTermChildrenById(Onto,"MS_1000031")
instruments <- vector()
for(i in 1:length(instrumentTerms)){
- instruments[i] <- getLabel(instrumentTerms[[i]])
+ instruments[i] <- ontoCAT::getLabel(instrumentTerms[[i]])
}
return(instruments)
}
@@ -176,9 +176,8 @@ smiles2mass <- function(SMILES){
}
.unitTestRMB <- function(WD=getwd()){
- require(RUnit)
- library(RMassBank)
- require(RMassBankData)
+ requireNamespace("RUnit",quietly=TRUE)
+ requireNamespace("RMassBankData",quietly=TRUE)
oldwd <- getwd()
setwd(WD)
w <- newMsmsWorkspace()
@@ -208,30 +207,29 @@ smiles2mass <- function(SMILES){
mb <- loadInfolists(mb, system.file("infolists", package="RMassBankData"))
mb <- mbWorkflow(mb)
- testSuite <- defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
+ testSuite <- RUnit::defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.EN_FC.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
- testSuite2 <- defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
+ testSuite2 <- RUnit::defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.DA.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
- testData <- suppressWarnings(runTestSuite(testSuite))
- testData2 <- suppressWarnings(runTestSuite(testSuite2))
+ testData <- suppressWarnings(RUnit::runTestSuite(testSuite))
+ testData2 <- suppressWarnings(RUnit::runTestSuite(testSuite2))
file.remove(c("pH_narcotics_Failpeaks.csv","pH_narcotics.RData","pH_narcotics_RA.RData","pH_narcotics_RF.RData"))
- printTextProtocol(testData)
- printTextProtocol(testData2)
+ RUnit::printTextProtocol(testData)
+ RUnit::printTextProtocol(testData2)
setwd(oldwd)
return(testData)
}
.unitTestRMB2 <- function(WD=getwd()){
- require(RUnit)
- library(RMassBank)
- require(RMassBankData)
+ requireNamespace("RUnit",quietly=TRUE)
+ requireNamespace("RMassBankData",quietly=TRUE)
oldwd <- getwd()
setwd(WD)
w <- newMsmsWorkspace()
@@ -264,22 +262,22 @@ smiles2mass <- function(SMILES){
mb <- loadInfolists(mb, system.file("infolists", package="RMassBankData"))
mb <- mbWorkflow(mb)
- testSuite <- defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
+ testSuite <- RUnit::defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.EN_FC.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
- testSuite2 <- defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
+ testSuite2 <- RUnit::defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.DA.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
- testData <- suppressWarnings(runTestSuite(testSuite))
- testData2 <- suppressWarnings(runTestSuite(testSuite2))
+ testData <- suppressWarnings(RUnit::runTestSuite(testSuite))
+ testData2 <- suppressWarnings(RUnit::runTestSuite(testSuite2))
file.remove(c("pH_narcotics_Failpeaks.csv","pH_narcotics.RData","pH_narcotics_RA.RData","pH_narcotics_RF.RData"))
- printTextProtocol(testData)
- printTextProtocol(testData2)
+ RUnit::printTextProtocol(testData)
+ RUnit::printTextProtocol(testData2)
setwd(oldwd)
return(testData)
}
\ No newline at end of file
diff --git a/R/zzz.R b/R/zzz.R
index 9885039bbc5b78829b39ef5bdd08c7b94fdcc6e0..b0a50f5a3275cb33161dfeebb2b909168d7f8fe0 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -4,4 +4,6 @@
RMassBank.env$testnumber <- 1
mb <- list()
attach(RMassBank.env)
-}
\ No newline at end of file
+}
+
+utils::globalVariables(c("cpdID", "isotopes","mzCalc"))
\ No newline at end of file
diff --git a/vignettes/RMassBankXCMS.Rnw b/vignettes/RMassBankXCMS.Rnw
index 92be3ead7e4d3517dc9d0f83bd5d2cbf6fa1f010..0cf6cbe69582ae827c54c3677082bca613348103 100644
--- a/vignettes/RMassBankXCMS.Rnw
+++ b/vignettes/RMassBankXCMS.Rnw
@@ -189,7 +189,7 @@ note that the naming of the csv has to be similar to the mzdata-files,
with the only difference being the filename extension. The readMethod
name for this is "peaklist"
-<<eval=FALSE>>=
+<<eval=TRUE>>=
msmsPeaklist <- newMsmsWorkspace()
msmsPeaklist@files <- list.files(system.file("spectra.Glucolesquerellin",
package = "RMassBankData"),