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