MS Data Analysis

Global functions
$,xcmsSet-method	Man page
$<-,xcmsSet-method	Man page
AutoLockMass	Man page
AutoLockMass,xcmsRaw-method	Man page
AutoLockMass-methods	Man page
CalibrantMassParam	Man page
CalibrantMassParam-class	Man page
CentWaveParam	Man page
CentWaveParam-class	Man page
CentWavePredIsoParam	Man page
CentWavePredIsoParam-class	Man page
FillChromPeaksParam	Man page
FillChromPeaksParam-class	Man page
GenericParam	Man page
GenericParam-class	Man page
MSW	Man page
MSWParam	Man page
MSWParam-class	Man page
MassifquantParam	Man page
MassifquantParam-class	Man page
MatchedFilterParam	Man page
MatchedFilterParam-class	Man page
MzClustParam	Man page
MzClustParam-class	Man page
NearestPeaksParam	Man page
NearestPeaksParam-class	Man page
ObiwarpParam	Man page
ObiwarpParam-class	Man page
PeakDensityParam	Man page
PeakDensityParam-class	Man page
PeakGroupsParam	Man page
PeakGroupsParam-class	Man page
ProcessHistory	Man page
ProcessHistory-class	Man page
SSgauss	Man page
XCMSnExp	Man page
XCMSnExp-class	Man page
XCMSnExp-filter	Man page
XChromatogram	Man page
XChromatogram-class	Man page
XChromatograms	Man page
XChromatograms-class	Man page
XProcessHistory	Man page
XProcessHistory-class	Man page
[,XCMSnExp,ANY,ANY,ANY-method	Man page
[,XChromatograms,ANY,ANY,ANY-method	Man page
[,xcmsRaw,logicalOrNumeric,missing,missing-method	Man page
[,xcmsSet,ANY,ANY,ANY-method	Man page
[,xcmsSet-method	Man page
[[,XCMSnExp,ANY,ANY-method	Man page
absMz	Man page
absMz,MzClustParam-method	Man page
absMz,NearestPeaksParam-method	Man page
absMz<-	Man page
absMz<-,MzClustParam-method	Man page
absMz<-,NearestPeaksParam-method	Man page
absRt	Man page
absRt,NearestPeaksParam-method	Man page
absRt<-	Man page
absRt<-,NearestPeaksParam-method	Man page
absent	Man page
absent,xcmsSet-method	Man page
addParams	Man page
addParams,MSWParam-method	Man page
addParams<-	Man page
addParams<-,MSWParam-method	Man page
adjustRtime	Man page
adjustRtime,OnDiskMSnExp,ObiwarpParam-method	Man page
adjustRtime,XCMSnExp,ObiwarpParam-method	Man page
adjustRtime,XCMSnExp,PeakGroupsParam-method	Man page
adjustRtime-obiwarp	Man page
adjustRtime-peakGroups	Man page
adjustRtimePeakGroups	Man page
adjustedRtime	Man page
adjustedRtime,MsFeatureData-method	Man page
adjustedRtime,XCMSnExp-method	Man page
adjustedRtime<-	Man page
adjustedRtime<-,MsFeatureData-method	Man page
adjustedRtime<-,XCMSnExp-method	Man page
ampTh	Man page
ampTh,MSWParam-method	Man page
ampTh<-	Man page
ampTh<-,MSWParam-method	Man page
applyAdjustedRtime	Man page
baseValue	Man page
baseValue,MatchedFilterParam-method	Man page
baseValue<-	Man page
baseValue<-,MatchedFilterParam-method	Man page
bin,XCMSnExp-method	Man page
binSize	Man page
binSize,MatchedFilterParam-method	Man page
binSize,ObiwarpParam-method	Man page
binSize,PeakDensityParam-method	Man page
binSize<-	Man page
binSize<-,MatchedFilterParam-method	Man page
binSize<-,ObiwarpParam-method	Man page
binSize<-,PeakDensityParam-method	Man page
binYonX	Man page
breaks_on_binSize	Man page
breaks_on_nBins	Man page
bw	Man page
bw,PeakDensityParam-method	Man page
bw<-	Man page
bw<-,PeakDensityParam-method	Man page
c, c-methods	Man page
c.XCMSnExp	Man page
c.xcmsSet	Man page
calibrate	Man page
calibrate,XCMSnExp-method	Man page
calibrate,xcmsSet-method	Man page
centWave	Man page
centWaveWithPredIsoROIs	Man page
centerSample	Man page
centerSample,ObiwarpParam-method	Man page
centerSample<-	Man page
centerSample<-,ObiwarpParam-method	Man page
checkBack	Man page
checkBack,MassifquantParam-method	Man page
checkBack<-	Man page
checkBack<-,MassifquantParam-method	Man page
chromPeakSpectra	Man page
chromPeaks	Man page
chromPeaks,MsFeatureData-method	Man page
chromPeaks,XCMSnExp-method	Man page
chromPeaks,XChromatogram-method	Man page
chromPeaks,XChromatograms-method	Man page
chromPeaks<-	Man page
chromPeaks<-,MsFeatureData-method	Man page
chromPeaks<-,XCMSnExp-method	Man page
chromPeaks<-,XChromatogram-method	Man page
chromatogram	Man page
chromatogram,XCMSnExp-method	Man page
chromatographic-peak-detection	Man page
clean,XCMSnExp-method	Man page
coerce,Chromatograms,XChromatograms-method	Man page
colMax	Man page
collect	Man page
collect,xcmsFragments-method	Man page
collect,xcmsRaw-method	Man page
collect-methods	Man page
consecMissedLimit	Man page
consecMissedLimit,MassifquantParam-method	Man page
consecMissedLimit<-	Man page
consecMissedLimit<-,MassifquantParam-method	Man page
criticalValue	Man page
criticalValue,MassifquantParam-method	Man page
criticalValue<-	Man page
criticalValue<-,MassifquantParam-method	Man page
deepCopy	Man page
deepCopy,xcmsRaw-method	Man page
descendMin	Man page
descendValue	Man page
descendZero	Man page
diffreport	Man page
diffreport,xcmsSet-method	Man page
distFun	Man page
distFun,ObiwarpParam-method	Man page
distFun<-	Man page
distFun<-,ObiwarpParam-method	Man page
distance	Man page
distance,MatchedFilterParam-method	Man page
distance<-	Man page
distance<-,MatchedFilterParam-method	Man page
do_adjustRtime_peakGroups	Man page
do_findChromPeaks_addPredIsoROIs	Man page
do_findChromPeaks_centWave	Man page
do_findChromPeaks_centWaveWithPredIsoROIs	Man page
do_findChromPeaks_massifquant	Man page
do_findChromPeaks_matchedFilter	Man page
do_findPeaks_MSW	Man page
do_groupChromPeaks_density	Man page
do_groupChromPeaks_nearest	Man page
do_groupPeaks_mzClust	Man page
doubleMatrix	Man page
dropAdjustedRtime	Man page
dropAdjustedRtime,MsFeatureData-method	Man page
dropAdjustedRtime,XCMSnExp-method	Man page
dropChromPeaks	Man page
dropChromPeaks,MsFeatureData-method	Man page
dropChromPeaks,XCMSnExp-method	Man page
dropFeatureDefinitions	Man page
dropFeatureDefinitions,MsFeatureData-method	Man page
dropFeatureDefinitions,XCMSnExp-method	Man page
dropFeatureDefinitions,XChromatograms-method	Man page
dropFilledChromPeaks	Man page
dropFilledChromPeaks,XCMSnExp-method	Man page
dropFilledChromPeaks,XChromatogram-method	Man page
dropFilledChromPeaks,XChromatograms-method	Man page
etg	Man page
expandMz	Man page
expandMz,FillChromPeaksParam-method	Man page
expandMz<-	Man page
expandMz<-,FillChromPeaksParam-method	Man page
expandRt	Man page
expandRt,FillChromPeaksParam-method	Man page
expandRt<-	Man page
expandRt<-,FillChromPeaksParam-method	Man page
exportMetaboAnalyst	Man page
extraPeaks	Man page
extraPeaks,PeakGroupsParam-method	Man page
extraPeaks<-	Man page
extraPeaks<-,PeakGroupsParam-method	Man page
extractChromatograms	Man page
extractChromatograms,OnDiskMSnExp-method	Man page
extractChromatograms,XCMSnExp-method	Man page
extractMsData	Man page
extractMsData,OnDiskMSnExp-method	Man page
extractMsData,XCMSnExp-method	Man page
factorDiag	Man page
factorDiag,ObiwarpParam-method	Man page
factorDiag<-	Man page
factorDiag<-,ObiwarpParam-method	Man page
factorGap	Man page
factorGap,ObiwarpParam-method	Man page
factorGap<-	Man page
factorGap<-,ObiwarpParam-method	Man page
family	Man page
family,PeakGroupsParam-method	Man page
family<-	Man page
family<-,PeakGroupsParam-method	Man page
featureChromatograms	Man page
featureDefinitions	Man page
featureDefinitions,MsFeatureData-method	Man page
featureDefinitions,XCMSnExp-method	Man page
featureDefinitions,XChromatograms-method	Man page
featureDefinitions<-	Man page
featureDefinitions<-,MsFeatureData-method	Man page
featureDefinitions<-,XCMSnExp-method	Man page
featureSpectra	Man page
featureSummary	Man page
featureValues	Man page
featureValues,XCMSnExp-method	Man page
featureValues,XChromatograms-method	Man page
fileIndex	Man page
fileIndex,ProcessHistory-method	Man page
filepaths	Man page
filepaths,xcmsSet-method	Man page
filepaths<-	Man page
filepaths<-,xcmsSet-method	Man page
fillChromPeaks	Man page
fillChromPeaks,XCMSnExp,FillChromPeaksParam-method	Man page
fillChromPeaks,XCMSnExp,missing-method	Man page
fillPeaks	Man page
fillPeaks,xcmsSet-method	Man page
fillPeaks-methods	Man page
fillPeaks.MSW	Man page
fillPeaks.MSW,xcmsSet-method	Man page
fillPeaks.MSW-methods	Man page
fillPeaks.chrom	Man page
fillPeaks.chrom,xcmsSet-method	Man page
fillPeaks.chrom-methods	Man page
filterAcquisitionNum,XCMSnExp-method	Man page
filterFeatureDefinitions	Man page
filterFile,XCMSnExp-method	Man page
filterMsLevel,XCMSnExp-method	Man page
filterMz,XCMSnExp-method	Man page
filterMz,XChromatogram-method	Man page
filterMz,XChromatograms-method	Man page
filterRt,XCMSnExp-method	Man page
filterRt,XChromatogram-method	Man page
filterRt,XChromatograms-method	Man page
filtfft	Man page
findChromPeaks	Man page
findChromPeaks,Chromatogram,CentWaveParam-method	Man page
findChromPeaks,Chromatogram,MatchedFilterParam-method	Man page
findChromPeaks,Chromatograms,CentWaveParam-method	Man page
findChromPeaks,Chromatograms,MatchedFilterParam-method	Man page
findChromPeaks,OnDiskMSnExp,CentWaveParam-method	Man page
findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam-method	Man page
findChromPeaks,OnDiskMSnExp,MSWParam-method	Man page
findChromPeaks,OnDiskMSnExp,MassifquantParam-method	Man page
findChromPeaks,OnDiskMSnExp,MatchedFilterParam-method	Man page
findChromPeaks,XCMSnExp,Param-method	Man page
findChromPeaks-Chromatogram-CentWaveParam	Man page
findChromPeaks-centWave	Man page
findChromPeaks-centWaveWithPredIsoROIs	Man page
findChromPeaks-massifquant	Man page
findChromPeaks-matchedFilter	Man page
findEqualGreater	Man page
findEqualGreaterM	Man page
findEqualLess	Man page
findMZ	Man page
findMZ,xcmsFragments-method	Man page
findPeaks	Man page
findPeaks,xcmsRaw-method	Man page
findPeaks-MSW	Man page
findPeaks-methods	Man page
findPeaks.MS1	Man page
findPeaks.MS1,xcmsRaw-method	Man page
findPeaks.MSW	Man page
findPeaks.MSW,xcmsRaw-method	Man page
findPeaks.addPredictedIsotopeFeatures	Man page
findPeaks.addPredictedIsotopeFeatures,xcmsRaw-method	Man page
findPeaks.centWave	Man page
findPeaks.centWave,xcmsRaw-method	Man page
findPeaks.centWaveWithPredictedIsotopeROIs	Man page
findPeaks.centWaveWithPredictedIsotopeROIs,xcmsRaw-method	Man page
findPeaks.massifquant	Man page
findPeaks.massifquant,xcmsRaw-method	Man page
findPeaks.matchedFilter	Man page
findPeaks.matchedFilter,xcmsRaw-method	Man page
findRange	Man page
findneutral	Man page
findneutral,xcmsFragments-method	Man page
firstBaselineCheck	Man page
firstBaselineCheck,CentWaveParam-method	Man page
firstBaselineCheck<-	Man page
firstBaselineCheck<-,CentWaveParam-method	Man page
fitgauss	Man page
fitgauss,CentWaveParam-method	Man page
fitgauss,MassifquantParam-method	Man page
fitgauss<-	Man page
fitgauss<-,CentWaveParam-method	Man page
fitgauss<-,MassifquantParam-method	Man page
fixedMz	Man page
fixedRt	Man page
fwhm	Man page
fwhm,MatchedFilterParam-method	Man page
fwhm<-	Man page
fwhm<-,MatchedFilterParam-method	Man page
gapExtend	Man page
gapExtend,ObiwarpParam-method	Man page
gapExtend<-	Man page
gapExtend<-,ObiwarpParam-method	Man page
gapInit	Man page
gapInit,ObiwarpParam-method	Man page
gapInit<-	Man page
gapInit<-,ObiwarpParam-method	Man page
getEIC	Man page
getEIC,xcmsRaw-method	Man page
getEIC,xcmsSet-method	Man page
getEIC-methods	Man page Man page
getMsnScan	Man page
getMsnScan,xcmsRaw-method	Man page
getPeaks	Man page
getPeaks,xcmsRaw-method	Man page
getPeaks-methods	Man page
getScan	Man page
getScan,xcmsRaw-method	Man page
getSpec	Man page
getSpec,xcmsRaw-method	Man page
getSpec-methods	Man page
getXcmsRaw	Man page
getXcmsRaw,xcmsSet-method	Man page
group	Man page
group,xcmsSet-method	Man page
group-methods	Man page
group.density	Man page
group.density,xcmsSet-method	Man page
group.mzClust	Man page
group.mzClust,xcmsSet-method	Man page
group.nearest	Man page
group.nearest,xcmsSet-method	Man page
groupChromPeaks	Man page
groupChromPeaks,XCMSnExp,MzClustParam-method	Man page
groupChromPeaks,XCMSnExp,NearestPeaksParam-method	Man page
groupChromPeaks,XCMSnExp,PeakDensityParam-method	Man page
groupChromPeaks,XChromatograms,PeakDensityParam-method	Man page
groupChromPeaks-density	Man page
groupChromPeaks-mzClust	Man page
groupChromPeaks-nearest	Man page
groupidx	Man page
groupidx,xcmsSet-method	Man page
groupidx<-	Man page
groupidx<-,xcmsSet-method	Man page
groupnames	Man page
groupnames,XCMSnExp-method	Man page
groupnames,xcmsEIC-method	Man page
groupnames,xcmsSet-method	Man page
groupnames-methods	Man page
groups	Man page
groups,xcmsSet-method	Man page
groups<-	Man page
groups<-,xcmsSet-method	Man page
groupval	Man page
groupval,xcmsSet-method	Man page
groupval-methods	Man page
hasAdjustedRtime	Man page
hasAdjustedRtime,MsFeatureData-method	Man page
hasAdjustedRtime,OnDiskMSnExp-method	Man page
hasAdjustedRtime,XCMSnExp-method	Man page
hasChromPeaks	Man page
hasChromPeaks,MsFeatureData-method	Man page
hasChromPeaks,XCMSnExp-method	Man page
hasChromPeaks,XChromatogram-method	Man page
hasChromPeaks,XChromatograms-method	Man page
hasFeatures	Man page
hasFeatures,MsFeatureData-method	Man page
hasFeatures,XCMSnExp-method	Man page
hasFeatures,XChromatograms-method	Man page
hasFilledChromPeaks	Man page
highlightChromPeaks	Man page
image,xcmsRaw-method	Man page
impute,MatchedFilterParam-method	Man page
impute<-	Man page
impute<-,MatchedFilterParam-method	Man page
imputeLinInterpol	Man page
imputeRowMin	Man page
imputeRowMinRand	Man page
index	Man page
index,MatchedFilterParam-method	Man page
index<-	Man page
index<-,MatchedFilterParam-method	Man page
initPenalty	Man page
initPenalty,ObiwarpParam-method	Man page
initPenalty<-	Man page
initPenalty<-,ObiwarpParam-method	Man page
integerMatrix	Man page
integrate,CentWaveParam-method	Man page
integrate,MassifquantParam-method	Man page
integrate<-	Man page
integrate<-,CentWaveParam-method	Man page
integrate<-,MassifquantParam-method	Man page
intensity,XCMSnExp-method	Man page
isCalibrated	Man page
kNN	Man page
kNN,NearestPeaksParam-method	Man page
kNN<-	Man page
kNN<-,NearestPeaksParam-method	Man page
levelplot	Man page
levelplot,xcmsRaw-method	Man page
levelplot,xcmsSet-method	Man page
loadRaw	Man page
loadRaw,xcmsFileSource-method	Man page
loadRaw,xcmsSource-method	Man page
loadRaw-methods	Man page
localAlignment	Man page
localAlignment,ObiwarpParam-method	Man page
localAlignment<-	Man page
localAlignment<-,ObiwarpParam-method	Man page
logicalMatrix	Man page
makeacqNum	Man page
makeacqNum, xcmsRaw-method	Man page
massifquant	Man page
matchedFilter	Man page
max,MatchedFilterParam-method	Man page
max<-	Man page
max<-,MatchedFilterParam-method	Man page
maxCharge	Man page
maxCharge,CentWavePredIsoParam-method	Man page
maxCharge<-	Man page
maxCharge<-,CentWavePredIsoParam-method	Man page
maxFeatures	Man page
maxFeatures,PeakDensityParam-method	Man page
maxFeatures<-	Man page
maxFeatures<-,PeakDensityParam-method	Man page
maxIso	Man page
maxIso,CentWavePredIsoParam-method	Man page
maxIso<-	Man page
maxIso<-,CentWavePredIsoParam-method	Man page
medianFilter	Man page
minFraction	Man page
minFraction,MzClustParam-method	Man page
minFraction,PeakDensityParam-method	Man page
minFraction,PeakGroupsParam-method	Man page
minFraction<-	Man page
minFraction<-,MzClustParam-method	Man page
minFraction<-,PeakDensityParam-method	Man page
minFraction<-,PeakGroupsParam-method	Man page
minNoiseLevel	Man page
minNoiseLevel,MSWParam-method	Man page
minNoiseLevel<-	Man page
minNoiseLevel<-,MSWParam-method	Man page
minSamples	Man page
minSamples,MzClustParam-method	Man page
minSamples,PeakDensityParam-method	Man page
minSamples<-	Man page
minSamples<-,MzClustParam-method	Man page
minSamples<-,PeakDensityParam-method	Man page
msLevel,XProcessHistory-method	Man page
mslevel	Man page
mslevel,xcmsRaw-method	Man page
mslevel,xcmsSet-method	Man page
msn2xcmsRaw	Man page
mz,CalibrantMassParam	Man page
mz,XCMSnExp-method	Man page
mzCenterFun	Man page
mzCenterFun,CentWaveParam-method	Man page
mzCenterFun,MassifquantParam-method	Man page
mzCenterFun<-	Man page
mzCenterFun<-,CentWaveParam-method	Man page
mzCenterFun<-,MassifquantParam-method	Man page
mzIntervalExtension	Man page
mzIntervalExtension,CentWavePredIsoParam-method	Man page
mzIntervalExtension<-	Man page
mzIntervalExtension<-,CentWavePredIsoParam-method	Man page
mzVsRtBalance	Man page
mzVsRtBalance,NearestPeaksParam-method	Man page
mzVsRtBalance<-	Man page
mzVsRtBalance<-,NearestPeaksParam-method	Man page
mzdiff	Man page
mzdiff,CentWaveParam-method	Man page
mzdiff,MassifquantParam-method	Man page
mzdiff,MatchedFilterParam-method	Man page
mzdiff<-	Man page
mzdiff<-,CentWaveParam-method	Man page
mzdiff<-,MassifquantParam-method	Man page
mzdiff<-,MatchedFilterParam-method	Man page
mzrange	Man page
mzrange,xcmsEIC-method	Man page
na.flatfill	Man page
nearbyPeak	Man page
nearbyPeak,MSWParam-method	Man page
nearbyPeak<-	Man page
nearbyPeak<-,MSWParam-method	Man page
noise	Man page
noise,CentWaveParam-method	Man page
noise,MassifquantParam-method	Man page
noise<-	Man page
noise<-,CentWaveParam-method	Man page
noise<-,MassifquantParam-method	Man page
normalize,XCMSnExp-method	Man page
overlappingFeatures	Man page
panel.cor	Man page
peakGroupsMatrix	Man page
peakGroupsMatrix,PeakGroupsParam-method	Man page
peakGroupsMatrix<-	Man page
peakGroupsMatrix<-,PeakGroupsParam-method	Man page
peakPlots,xcmsSet-method	Man page
peakPlots-methods	Man page
peakScaleRange	Man page
peakScaleRange,MSWParam-method	Man page
peakScaleRange<-	Man page
peakScaleRange<-,MSWParam-method	Man page
peakTable	Man page
peakTable,xcmsSet-method	Man page
peakThr	Man page
peakThr,MSWParam-method	Man page
peakThr<-	Man page
peakThr<-,MSWParam-method	Man page
peaks	Man page
peaks,xcmsSet-method	Man page
peaks<-	Man page
peaks<-,xcmsSet-method	Man page
peaksWithCentWave	Man page
peaksWithMatchedFilter	Man page
peakwidth	Man page
peakwidth,CentWaveParam-method	Man page
peakwidth,MassifquantParam-method	Man page
peakwidth<-	Man page
peakwidth<-,CentWaveParam-method	Man page
peakwidth<-,MassifquantParam-method	Man page
phenoData	Man page
phenoData,xcmsSet-method	Man page
phenoData<-	Man page
phenoData<-,xcmsSet,ANY-method	Man page
phenoData<-,xcmsSet-method	Man page
phenoDataFromPaths	Man page
pickPeaks,XCMSnExp-method	Man page
plot, plot-methods	Man page
plot,XChromatogram,ANY-method	Man page
plot,XChromatograms,ANY-method	Man page
plot.xcmsEIC	Man page
plotAdjustedRtime	Man page
plotChrom	Man page
plotChrom,xcmsRaw-method	Man page
plotChrom-methods	Man page
plotChromPeakDensity	Man page
plotChromPeakDensity,XCMSnExp-method	Man page
plotChromPeakDensity,XChromatograms-method	Man page
plotChromPeakImage	Man page
plotChromPeaks	Man page
plotChromatogram	Man page
plotEIC	Man page
plotEIC,xcmsRaw-method	Man page
plotMsData	Man page
plotPeaks	Man page
plotPeaks,xcmsRaw-method	Man page
plotPeaks-methods	Man page
plotQC	Man page
plotRaw	Man page
plotRaw,xcmsRaw-method	Man page
plotRaw-methods	Man page
plotScan	Man page
plotScan,xcmsRaw-method	Man page
plotScan-methods	Man page
plotSpec	Man page
plotSpec,xcmsRaw-method	Man page
plotSpec-methods	Man page
plotSurf	Man page
plotSurf,xcmsRaw-method	Man page
plotSurf-methods	Man page
plotTIC	Man page
plotTIC,xcmsRaw-method	Man page
plotTIC-methods	Man page
plotTree	Man page
plotTree,xcmsFragments-method	Man page
plotrt	Man page
plotrt,xcmsSet-method	Man page
plotrt-methods	Man page
polarity,CentWavePredIsoParam-method	Man page
polarity<-	Man page
polarity<-,CentWavePredIsoParam-method	Man page
ppm	Man page
ppm,CentWaveParam-method	Man page
ppm,FillChromPeaksParam-method	Man page
ppm,MassifquantParam-method	Man page
ppm,MzClustParam-method	Man page
ppm<-	Man page
ppm<-,CentWaveParam-method	Man page
ppm<-,FillChromPeaksParam-method	Man page
ppm<-,MassifquantParam-method	Man page
ppm<-,MzClustParam-method	Man page
prefilter	Man page
prefilter,CentWaveParam-method	Man page
prefilter,MassifquantParam-method	Man page
prefilter<-	Man page
prefilter<-,CentWaveParam-method	Man page
prefilter<-,MassifquantParam-method	Man page
present	Man page
present,xcmsSet-method	Man page
processDate	Man page
processDate,ProcessHistory-method	Man page
processHistory	Man page
processHistory,XCMSnExp-method	Man page
processHistory,XChromatograms-method	Man page
processHistoryTypes	Man page
processInfo	Man page
processInfo,ProcessHistory-method	Man page
processParam	Man page
processParam,XProcessHistory-method	Man page
processType	Man page
processType,ProcessHistory-method	Man page
profBin	Man page
profBinLin	Man page
profBinLinBase	Man page
profBinLinBaseM	Man page
profBinLinM	Man page
profBinM	Man page
profIntLin	Man page
profIntLinM	Man page
profMat	Man page
profMat,OnDiskMSnExp-method	Man page
profMat,XCMSnExp-method	Man page
profMat,xcmsRaw-method	Man page
profMat-xcmsSet	Man page
profMaxIdx	Man page
profMaxIdxM	Man page
profMedFilt	Man page
profMedFilt,xcmsRaw-method	Man page
profMedFilt-methods	Man page
profMethod	Man page
profMethod,xcmsRaw-method	Man page
profMethod,xcmsSet-method	Man page
profMethod-methods	Man page
profMethod<-	Man page
profMethod<-,xcmsRaw-method	Man page
profMethod<--methods	Man page
profMz	Man page
profMz,xcmsRaw-method	Man page
profRange	Man page
profRange,xcmsRaw-method	Man page
profRange-methods	Man page
profStep	Man page
profStep,xcmsRaw-method	Man page
profStep,xcmsSet-method	Man page
profStep-methods	Man page
profStep<-	Man page
profStep<-,xcmsRaw-method	Man page
profStep<--methods	Man page
profile-matrix	Man page
profinfo	Man page
profinfo,xcmsRaw-method	Man page
profinfo,xcmsSet-method	Man page
profinfo<-	Man page
profinfo<-,xcmsSet-method	Man page
progressCallback	Man page
progressCallback,xcmsSet-method	Man page
progressCallback<-	Man page
progressCallback<-,xcmsSet-method	Man page
pval	Man page
rawEIC	Man page
rawEIC,xcmsRaw-method	Man page
rawMat	Man page
rawMat,xcmsRaw-method	Man page
rawMat-methods	Man page
rectUnique	Man page
removePeaks,XCMSnExp-method	Man page
response	Man page
response,ObiwarpParam-method	Man page
response<-	Man page
response<-,ObiwarpParam-method	Man page
retcor	Man page
retcor,xcmsSet-method	Man page
retcor-methods	Man page
retcor.linear	Man page
retcor.linear,xcmsSet-method	Man page
retcor.loess	Man page
retcor.loess,xcmsSet-method	Man page
retcor.obiwarp	Man page
retcor.obiwarp,xcmsSet-method	Man page
retcor.peakgroups	Man page
retcor.peakgroups,xcmsSet-method	Man page
retexp	Man page
revMz	Man page
revMz,xcmsRaw-method	Man page
ridgeLength	Man page
ridgeLength,MSWParam-method	Man page
ridgeLength<-	Man page
ridgeLength<-,MSWParam-method	Man page
rla	Man page
roiList	Man page
roiList,CentWaveParam-method	Man page
roiList<-	Man page
roiList<-,CentWaveParam-method	Man page
roiScales	Man page
roiScales,CentWaveParam-method	Man page
roiScales<-	Man page
roiScales<-,CentWaveParam-method	Man page
rowMax	Man page
rowRla	Man page
rtime,XCMSnExp-method	Man page
rtrange	Man page
rtrange,xcmsEIC-method	Man page
sampclass	Man page
sampclass,xcmsSet-method	Man page
sampclass<-	Man page
sampclass<-,xcmsSet-method	Man page
sampleGroups	Man page
sampleGroups,MzClustParam-method	Man page
sampleGroups,NearestPeaksParam-method	Man page
sampleGroups,PeakDensityParam-method	Man page
sampleGroups<-	Man page
sampleGroups<-,MzClustParam-method	Man page
sampleGroups<-,NearestPeaksParam-method	Man page
sampleGroups<-,PeakDensityParam-method	Man page
sampnames	Man page
sampnames,xcmsEIC-method	Man page
sampnames,xcmsSet-method	Man page
sampnames-methods	Man page
sampnames<-	Man page
sampnames<-,xcmsSet-method	Man page
scales	Man page
scales,MSWParam-method	Man page
scales<-	Man page
scales<-,MSWParam-method	Man page
scanrange	Man page
scanrange,xcmsRaw-method	Man page
scanrange,xcmsSet-method	Man page
setAs	Man page
show,CentWaveParam-method	Man page
show,CentWavePredIsoParam-method	Man page
show,FillChromPeaksParam-method	Man page
show,GenericParam-method	Man page
show,MSWParam-method	Man page
show,MassifquantParam-method	Man page
show,MatchedFilterParam-method	Man page
show,MsFeatureData-method	Man page
show,MzClustParam-method	Man page
show,NearestPeaksParam-method	Man page
show,ObiwarpParam-method	Man page
show,PeakDensityParam-method	Man page
show,PeakGroupsParam-method	Man page
show,ProcessHistory-method	Man page
show,XCMSnExp-method	Man page
show,XChromatogram-method	Man page
show,XChromatograms-method	Man page
show,XProcessHistory-method	Man page
show,xcmsEIC-method	Man page
show,xcmsFragments-method	Man page
show,xcmsPeaks-method	Man page
show,xcmsRaw-method	Man page
show,xcmsSet-method	Man page
showError	Man page
showError,xcmsSet-method	Man page
sigma	Man page
sigma,MatchedFilterParam-method	Man page
sigma<-	Man page
sigma<-,MatchedFilterParam-method	Man page
smooth	Man page
smooth,PeakGroupsParam-method	Man page
smooth,XCMSnExp-method	Man page
smooth<-	Man page
smooth<-,PeakGroupsParam-method	Man page
snthresh	Man page
snthresh,CentWaveParam-method	Man page
snthresh,MSWParam-method	Man page
snthresh,MassifquantParam-method	Man page
snthresh,MatchedFilterParam-method	Man page
snthresh<-	Man page
snthresh<-,CentWaveParam-method	Man page
snthresh<-,MSWParam-method	Man page
snthresh<-,MassifquantParam-method	Man page
snthresh<-,MatchedFilterParam-method	Man page
snthreshIsoROIs	Man page
snthreshIsoROIs,CentWavePredIsoParam-method	Man page
snthreshIsoROIs<-	Man page
snthreshIsoROIs<-,CentWavePredIsoParam-method	Man page
sortMz	Man page
sortMz,xcmsRaw-method	Man page
span	Man page
span,PeakGroupsParam-method	Man page
span<-	Man page
span<-,PeakGroupsParam-method	Man page
specDist	Man page
specDist,xcmsSet-method	Man page
specDist-methods	Man page
specDist.cosine	Man page
specDist.cosine,matrix,matrix-method	Man page
specDist.meanMZmatch	Man page
specDist.meanMZmatch,matrix,matrix-method	Man page
specDist.peakCount	Man page
specDist.peakCount,matrix,matrix-method	Man page
specDist.peakCount-methods	Man page
specNoise	Man page
specPeaks	Man page
spectra,XCMSnExp-method	Man page
spectrapply,XCMSnExp-method	Man page
split, split-methods	Man page
split,XCMSnExp,ANY-method	Man page
split.xcmsRaw	Man page
split.xcmsSet	Man page
steps	Man page
steps,MatchedFilterParam-method	Man page
steps<-	Man page
steps<-,MatchedFilterParam-method	Man page
stitch	Man page
stitch,xcmsRaw-method	Man page
stitch-methods	Man page
stitch.netCDF	Man page
stitch.xml	Man page
subset	Man page
subset,ObiwarpParam-method	Man page
subset,PeakGroupsParam-method	Man page
subset-xcmsRaw	Man page
subset<-	Man page
subset<-,ObiwarpParam-method	Man page
subset<-,PeakGroupsParam-method	Man page
subsetAdjust	Man page
subsetAdjust,ObiwarpParam-method	Man page
subsetAdjust,PeakGroupsParam-method	Man page
subsetAdjust<-	Man page
subsetAdjust<-,ObiwarpParam-method	Man page
subsetAdjust<-,PeakGroupsParam-method	Man page
tuneIn	Man page
tuneIn,MSWParam-method	Man page
tuneIn<-	Man page
tuneIn<-,MSWParam-method	Man page
unions	Man page
unions,MassifquantParam-method	Man page
unions<-	Man page
unions<-,MassifquantParam-method	Man page
updateObject,xcmsSet-method	Man page
useOriginalCode	Man page
verboseColumns	Man page
verboseColumns,CentWaveParam-method	Man page
verboseColumns,MSWParam-method	Man page
verboseColumns,MassifquantParam-method	Man page
verboseColumns<-	Man page
verboseColumns<-,CentWaveParam-method	Man page
verboseColumns<-,MSWParam-method	Man page
verboseColumns<-,MassifquantParam-method	Man page
verify.mzQuantML	Man page
which.colMax	Man page
which.rowMax	Man page
withWave	Man page
withWave,MassifquantParam-method	Man page
withWave<-	Man page
withWave<-,MassifquantParam-method	Man page
write.cdf	Man page
write.cdf,xcmsRaw-method	Man page
write.mzQuantML	Man page
write.mzQuantML,xcmsSet-method	Man page
write.mzdata	Man page
write.mzdata,xcmsRaw-method	Man page
writeMSData,XCMSnExp,character-method	Man page
writeMzTab	Man page
xcms-deprecated	Man page
xcmsEIC-class	Man page
xcmsFileSource-class	Man page
xcmsFragments	Man page
xcmsFragments-class	Man page
xcmsPapply	Man page
xcmsPeaks-class	Man page
xcmsRaw	Man page
xcmsRaw-class	Man page
xcmsSet	Man page
xcmsSet-class	Man page
xcmsSource	Man page
xcmsSource,character-method	Man page
xcmsSource,xcmsSource-method	Man page
xcmsSource-class	Man page
xcmsSource-methods	Man page