diff --git a/DESCRIPTION b/DESCRIPTION
index 8cd1d156ea91576f440dc3d6771cfe69712c3637..5f46eca1efab0e58a02c93982a074acc7f381d49 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: RMassBank
Type: Package
Title: Workflow to process tandem MS files and build MassBank records
-Version: 1.99.6
+Version: 1.99.7
Authors@R: c(
person(given = "RMassBank at Eawag", email = "massbank@eawag.ch",
role=c("cre")),
diff --git a/R/alternateAnalyze.R b/R/alternateAnalyze.R
index a3c75bbaa3e9a0c05aaf431064771ac1a5212199..c708634b66a65d8701ced4c6626d3d042e4b70dc 100644
--- a/R/alternateAnalyze.R
+++ b/R/alternateAnalyze.R
@@ -296,8 +296,8 @@ analyzeMsMs.formula.optimized <- function(msmsPeaks, mode="pH", detail=FALSE, ru
# Circumvent bug in rcdk: correct the mass for the charge first, then calculate uncharged formulae
# finally back-correct calculated masses for the charge
mass.calc <- mass + mode.charge * .emass
- peakformula <- tryCatch(generate.formula(mass.calc, ppm(mass.calc, ppmlimit, p=TRUE),
- limits, charge=0), error=function(e) NA)
+ peakformula <- tryCatch(suppressWarnings(generate.formula(mass.calc, ppm(mass.calc, ppmlimit, p=TRUE),
+ limits, charge=0)), error=function(e) NA)
#peakformula <- tryCatch(
# generate.formula(mass,
# ppm(mass, ppmlimit, p=TRUE),
@@ -327,8 +327,8 @@ analyzeMsMs.formula.optimized <- function(msmsPeaks, mode="pH", detail=FALSE, ru
# Circumvent bug in rcdk: correct the mass for the charge first, then calculate uncharged formulae
# finally back-correct calculated masses for the charge
mass.calc <- mass + mode.charge * .emass
- peakformula <- tryCatch(generate.formula(mass.calc, ppm(mass.calc, ppmlimit, p=TRUE),
- limits, charge=0), error=function(e) NA)
+ peakformula <- tryCatch(suppressWarnings(generate.formula(mass.calc, ppm(mass.calc, ppmlimit, p=TRUE),
+ limits, charge=0)), error=function(e) NA)
#peakformula <- tryCatch(
# generate.formula(mass,
# ppm(mass, ppmlimit, p=TRUE),
@@ -380,7 +380,7 @@ analyzeMsMs.formula.optimized <- function(msmsPeaks, mode="pH", detail=FALSE, ru
childPeaksInt <- merge(childPeaks, shot, by.x = "mzFound", by.y = mzColname, all.x = TRUE, all.y = FALSE )
# find the best ppm value
- bestPpm <- aggregate(childPeaksInt$dppm, list(childPeaksInt$mzFound),
+ bestPpm <- aggregate(as.data.frame(childPeaksInt$dppm), list(childPeaksInt$mzFound),
function(dppm) dppm[[which.min(abs(dppm))]])
colnames(bestPpm) <- c("mzFound", "dppmBest")
childPeaksInt <- merge(childPeaksInt, bestPpm, by="mzFound", all.x=TRUE)
diff --git a/R/leMsMs.r b/R/leMsMs.r
index 74e5c04efd09bbc1404935c119a874698dc82236..9e85bccf5629b42c2a5e488135aac7bda79d53cc 100755
--- a/R/leMsMs.r
+++ b/R/leMsMs.r
@@ -460,7 +460,6 @@ analyzeMsMs.formula <- function(msmsPeaks, mode="pH", detail=FALSE, run="prelimi
# MolgenMsMs
parentSpectrum <- msmsPeaks@parent
-
# On each spectrum the following function analyzeTandemShot will be applied.
# It takes the raw peaks matrix as argument (mz, int) and processes the spectrum by
@@ -508,7 +507,6 @@ analyzeMsMs.formula <- function(msmsPeaks, mode="pH", detail=FALSE, run="prelimi
# this was done for the MOLGEN MSMS type analysis, is not necessary anymore now (23.1.15 MST)
# shot[,mzColname] <- round(shot[,mzColname], 5)
-
# here follows the Rcdk analysis
#------------------------------------
parentPeaks <- data.frame(mzFound=msmsPeaks@mz,
@@ -574,8 +572,8 @@ analyzeMsMs.formula <- function(msmsPeaks, mode="pH", detail=FALSE, run="prelimi
# finally back-correct calculated masses for the charge
mass <- shot.row[["mz"]]
mass.calc <- mass + mode.charge * .emass
- peakformula <- tryCatch(generate.formula(mass.calc, ppm(mass.calc, ppmlimit, p=TRUE),
- limits, charge=0), error=function(e) NA)
+ peakformula <- tryCatch(suppressWarnings(generate.formula(mass.calc, ppm(mass.calc, ppmlimit, p=TRUE),
+ limits, charge=0)), error=function(e) NA)
#peakformula <- tryCatch(
# generate.formula(mass,
# ppm(mass, ppmlimit, p=TRUE),
@@ -650,9 +648,9 @@ analyzeMsMs.formula <- function(msmsPeaks, mode="pH", detail=FALSE, run="prelimi
child@ok <- FALSE
return(child)
}
-
+#browser()
# find the best ppm value
- bestPpm <- aggregate(childPeaks[!is.na(childPeaks$dppm),"dppm"],
+ bestPpm <- aggregate(as.data.frame(childPeaks[!is.na(childPeaks$dppm),"dppm"]),
list(childPeaks[!is.na(childPeaks$dppm),"row"]),
function(dppm) dppm[[which.min(abs(dppm))]])
colnames(bestPpm) <- c("row", "dppmBest")
@@ -1107,7 +1105,7 @@ problematicPeaks <- function(peaks_unmatched, peaks_matched, mode="pH")
if(nrow(peaks_matched) == 0){
assIntMax <- data.frame(list(integer(0),integer(0),integer(0)))
} else{
- assIntMax <- as.data.frame(aggregate(peaks_matched$intensity,
+ assIntMax <- as.data.frame(aggregate(as.data.frame(peaks_matched$intensity),
by=list(peaks_matched$cpdID, peaks_matched$scan), max))
}
colnames(assIntMax) <- c("cpdID", "scan", "aMax")
@@ -1336,6 +1334,8 @@ makeRecalibration <- function(w, mode,
plotRecalibration <- function(w, recalibrateBy = getOption("RMassBank")$recalibrateBy)
{
spec <- w@aggregated
+ if(!is.null(w@parent))
+ spec <- w@parent@aggregated
rcdata <- data.frame(mzFound = w@rc$x, recalfield = w@rc$y)
ms1data <- data.frame(mzFound = w@rc.ms1$x, recalfield = w@rc.ms1$y)
@@ -1718,8 +1718,8 @@ reanalyzeFailpeak <- function(custom_additions, mass, cpdID, counter, pb = NULL,
#print(parent_formula)
limits <- to.limits.rcdk(parent_formula)
- peakformula <- tryCatch(generate.formula(mass, ppm(mass, ppmlimit, p=TRUE),
- limits, charge=mode.charge), error=function(e) NA)
+ peakformula <- tryCatch(suppressWarnings(generate.formula(mass, ppm(mass, ppmlimit, p=TRUE),
+ limits, charge=mode.charge)), error=function(e) NA)
# was a formula found? If not, return empty result
if(!is.list(peakformula))
return(as.data.frame(
@@ -1834,7 +1834,8 @@ filterPeaksMultiplicity <- function(peaks, formulacol, recalcBest = TRUE)
else
{
# calculate duplicity info
- multInfo <- aggregate(peaks$scan, list(peaks$cpdID, peaks[,formulacol]), FUN=length)
+ multInfo <- aggregate(as.data.frame(peaks$scan),
+ list(peaks$cpdID, peaks[,formulacol]), FUN=length)
# just for comparison:
# nform <- unique(paste(pks$cpdID,pks$formula))
@@ -1877,7 +1878,7 @@ filterPeaksMultiplicity <- function(peaks, formulacol, recalcBest = TRUE)
# prioritize duplicate peaks
# get unique peaks with their maximum-multiplicity formula attached
- best_mult <- aggregate(peaks$formulaMultiplicity,
+ best_mult <- aggregate(as.data.frame(peaks$formulaMultiplicity),
list(peaks$cpdID, peaks$scan, peaks$mzFound),
max)
colnames(best_mult) <- c("cpdID", "scan", "mzFound", "bestMultiplicity")
@@ -1887,7 +1888,7 @@ filterPeaksMultiplicity <- function(peaks, formulacol, recalcBest = TRUE)
# now we also have to recalculate dppmBest since the "old best" may have been
# dropped.
peaks$dppmBest <- NULL
- bestPpm <- aggregate(peaks$dppm,
+ bestPpm <- aggregate(as.data.frame(peaks$dppm),
list(peaks$cpdID, peaks$scan, peaks$mzFound),
function(dppm) dppm[[which.min(abs(dppm))]])
colnames(bestPpm) <- c("cpdID", "scan", "mzFound", "dppmBest")
@@ -1899,7 +1900,7 @@ filterPeaksMultiplicity <- function(peaks, formulacol, recalcBest = TRUE)
pks_best$formulaMultiplicity <- NULL
pks_best$bestMultiplicity <- NULL
- multInfo_best <- aggregate(pks_best$scan,
+ multInfo_best <- aggregate(as.data.frame(pks_best$scan),
list(pks_best$cpdID, pks_best[,formulacol]),
FUN=length)
colnames(multInfo_best) <- c("cpdID", formulacol, "formulaMultiplicity")