$,xcmsSet-method	xcmsSet-class
$<-,xcmsSet-method	xcmsSet-class
absent	absent-methods
absent,xcmsSet-method	absent-methods
absMz	groupChromPeaks
absMz,MzClustParam-method	groupChromPeaks
absMz,NearestPeaksParam-method	groupChromPeaks
absMz<-	groupChromPeaks
absMz<-,MzClustParam-method	groupChromPeaks
absMz<-,NearestPeaksParam-method	groupChromPeaks
absRt	groupChromPeaks
absRt,NearestPeaksParam-method	groupChromPeaks
absRt<-	groupChromPeaks
absRt<-,NearestPeaksParam-method	groupChromPeaks
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,XcmsExperiment-method	XcmsExperiment
adjustedRtime,XCMSnExp-method	XCMSnExp-class
adjustedRtime<-	XCMSnExp-class
adjustedRtime<-,MsFeatureData-method	XCMSnExp-class
adjustedRtime<-,XCMSnExp-method	XCMSnExp-class
adjustRtime	adjustRtime
adjustRtime,MsExperiment,ObiwarpParam-method	adjustRtime
adjustRtime,MsExperiment,PeakGroupsParam-method	adjustRtime
adjustRtime,OnDiskMSnExp,ObiwarpParam-method	adjustRtime
adjustRtime,XcmsExperiment,LamaParama-method	LamaParama
adjustRtime,XCMSnExp,ObiwarpParam-method	adjustRtime
adjustRtime,XCMSnExp,PeakGroupsParam-method	adjustRtime
adjustRtimePeakGroups	adjustRtime
ampTh	findPeaks-MSW
ampTh,MSWParam-method	findPeaks-MSW
ampTh<-	findPeaks-MSW
ampTh<-,MSWParam-method	findPeaks-MSW
applyAdjustedRtime	applyAdjustedRtime
as.list,CentWaveParam-method	findChromPeaks-centWave
as.list,PeakDensityParam-method	groupChromPeaks
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
binSize,PeakDensityParam-method	groupChromPeaks
binSize<-	findChromPeaks-matchedFilter
binSize<-,MatchedFilterParam-method	findChromPeaks-matchedFilter
binSize<-,ObiwarpParam-method	adjustRtime
binSize<-,PeakDensityParam-method	groupChromPeaks
binYonX	binYonX
BlankFlag	BlankFlag
breaks_on_binSize	breaks_on_binSize
breaks_on_nBins	breaks_on_nBins
bw	groupChromPeaks
bw,PeakDensityParam-method	groupChromPeaks
bw<-	groupChromPeaks
bw<-,PeakDensityParam-method	groupChromPeaks
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
centerSample,ObiwarpParam-method	adjustRtime
centerSample<-	adjustRtime
centerSample<-,ObiwarpParam-method	adjustRtime
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,MsExperiment-method	XcmsExperiment
chromatogram,XcmsExperiment-method	XcmsExperiment
chromatogram,XCMSnExp-method	chromatogram-method
ChromPeakAreaParam	fillChromPeaks
ChromPeakAreaParam-class	fillChromPeaks
chromPeakChromatograms	chromPeakChromatograms
chromPeakChromatograms,XcmsExperiment-method	chromPeakChromatograms
chromPeakData	XCMSnExp-class
chromPeakData,MsFeatureData-method	XCMSnExp-class
chromPeakData,XChromatogram-method	XChromatogram
chromPeakData,XChromatograms-method	XChromatogram
chromPeakData,XcmsExperiment-method	XcmsExperiment
chromPeakData,XCMSnExp-method	XCMSnExp-class
chromPeakData<-	XCMSnExp-class
chromPeakData<-,MsFeatureData-method	XCMSnExp-class
chromPeakData<-,XChromatogram-method	XChromatogram
chromPeakData<-,XcmsExperiment-method	XcmsExperiment
chromPeakData<-,XCMSnExp-method	XCMSnExp-class
chromPeaks	XCMSnExp-class
chromPeaks,MsFeatureData-method	XCMSnExp-class
chromPeaks,XChromatogram-method	XChromatogram
chromPeaks,XChromatograms-method	XChromatogram
chromPeaks,XcmsExperiment-method	XcmsExperiment
chromPeaks,XCMSnExp-method	XCMSnExp-class
chromPeaks<-	XCMSnExp-class
chromPeaks<-,MsFeatureData-method	XCMSnExp-class
chromPeaks<-,XChromatogram-method	XChromatogram
chromPeaks<-,XcmsExperiment-method	XcmsExperiment
chromPeaks<-,XCMSnExp-method	XCMSnExp-class
chromPeakSpectra	chromPeakSpectra
chromPeakSpectra,XcmsExperiment-method	chromPeakSpectra
chromPeakSpectra,XCMSnExp-method	chromPeakSpectra
class:Param	GenericParam
clean,XCMSnExp-method	XCMSnExp-inherited-methods
CleanPeaksParam	refineChromPeaks
CleanPeaksParam-class	refineChromPeaks
coerce,MChromatograms,XChromatograms-method	XChromatogram
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
correlate	correlate-Chromatogram
correlate,Chromatogram,Chromatogram-method	correlate-Chromatogram
correlate,MChromatograms,MChromatograms-method	correlate-Chromatogram
correlate,MChromatograms,missing-method	correlate-Chromatogram
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
dirname	dirname
dirname,OnDiskMSnExp-method	dirname
dirname<-,OnDiskMSnExp-method	dirname
distance	findChromPeaks-matchedFilter
distance,MatchedFilterParam-method	findChromPeaks-matchedFilter
distance<-	findChromPeaks-matchedFilter
distance<-,MatchedFilterParam-method	findChromPeaks-matchedFilter
distFun	adjustRtime
distFun,ObiwarpParam-method	adjustRtime
distFun<-	adjustRtime
distFun<-,ObiwarpParam-method	adjustRtime
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
DratioFilter	DratioFilter
dropAdjustedRtime	XCMSnExp-class
dropAdjustedRtime,MsFeatureData-method	XCMSnExp-class
dropAdjustedRtime,XcmsExperiment-method	XcmsExperiment
dropAdjustedRtime,XCMSnExp-method	XCMSnExp-class
dropChromPeaks	XCMSnExp-class
dropChromPeaks,MsFeatureData-method	XCMSnExp-class
dropChromPeaks,XcmsExperiment-method	XcmsExperiment
dropChromPeaks,XCMSnExp-method	XCMSnExp-class
dropFeatureDefinitions	XCMSnExp-class
dropFeatureDefinitions,MsFeatureData-method	XCMSnExp-class
dropFeatureDefinitions,XChromatograms-method	XChromatogram
dropFeatureDefinitions,XcmsExperiment-method	XcmsExperiment
dropFeatureDefinitions,XCMSnExp-method	XCMSnExp-class
dropFilledChromPeaks	XCMSnExp-class
dropFilledChromPeaks,XChromatogram-method	XChromatogram
dropFilledChromPeaks,XChromatograms-method	XChromatogram
dropFilledChromPeaks,XcmsExperiment-method	XcmsExperiment
dropFilledChromPeaks,XCMSnExp-method	XCMSnExp-class
EicSimilarityParam	groupFeatures-eic-similarity
EicSimilarityParam-class	groupFeatures-eic-similarity
estimatePrecursorIntensity,MsExperiment-method	estimatePrecursorIntensity
estimatePrecursorIntensity,OnDiskMSnExp-method	estimatePrecursorIntensity
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
exportMetaboAnalyst	exportMetaboAnalyst
extractMsData	extractMsData-method
extractMsData,OnDiskMSnExp-method	extractMsData-method
extractMsData,XCMSnExp-method	extractMsData-method
extraPeaks	adjustRtime
extraPeaks,PeakGroupsParam-method	adjustRtime
extraPeaks<-	adjustRtime
extraPeaks<-,PeakGroupsParam-method	adjustRtime
faahko_sub	loadXcmsData
faahko_sub2	loadXcmsData
factorDiag	adjustRtime
factorDiag,ObiwarpParam-method	adjustRtime
factorDiag<-	adjustRtime
factorDiag<-,ObiwarpParam-method	adjustRtime
factorGap	adjustRtime
factorGap,ObiwarpParam-method	adjustRtime
factorGap<-	adjustRtime
factorGap<-,ObiwarpParam-method	adjustRtime
family	adjustRtime
family,PeakGroupsParam-method	adjustRtime
family<-	adjustRtime
family<-,PeakGroupsParam-method	adjustRtime
feature-grouping	feature-grouping
featureArea	XcmsExperiment
featureChromatograms	featureChromatograms
featureChromatograms,XcmsExperiment-method	featureChromatograms
featureChromatograms,XCMSnExp-method	featureChromatograms
featureDefinitions	XCMSnExp-class
featureDefinitions,MsFeatureData-method	XCMSnExp-class
featureDefinitions,XChromatograms-method	XChromatogram
featureDefinitions,XcmsExperiment-method	XcmsExperiment
featureDefinitions,XCMSnExp-method	XCMSnExp-class
featureDefinitions<-	XCMSnExp-class
featureDefinitions<-,MsFeatureData-method	XCMSnExp-class
featureDefinitions<-,XcmsExperiment-method	XcmsExperiment
featureDefinitions<-,XCMSnExp-method	XCMSnExp-class
featureGroups,XcmsResult-method	feature-grouping
featureGroups<-,XcmsResult-method	feature-grouping
featureSpectra	featureSpectra
featureSpectra,XcmsExperiment-method	featureSpectra
featureSpectra,XCMSnExp-method	featureSpectra
featureSummary	featureSummary
featureValues	XCMSnExp-peak-grouping-results
featureValues,XChromatograms-method	XChromatogram
featureValues,XcmsExperiment-method	XcmsExperiment
featureValues,XCMSnExp-method	XCMSnExp-peak-grouping-results
fileIndex	ProcessHistory-class
fileIndex,ProcessHistory-method	ProcessHistory-class
fileNames,MsExperiment-method	XcmsExperiment
filepaths	xcmsSet-class
filepaths,xcmsSet-method	xcmsSet-class
filepaths<-	xcmsSet-class
filepaths<-,xcmsSet-method	xcmsSet-class
fillChromPeaks	fillChromPeaks
fillChromPeaks,XcmsExperiment,ChromPeakAreaParam-method	fillChromPeaks
fillChromPeaks,XCMSnExp,ChromPeakAreaParam-method	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
filterChromPeaks	XcmsExperiment
filterChromPeaks,XChromatogram-method	XChromatogram
filterChromPeaks,XChromatograms-method	XChromatogram
filterChromPeaks,XcmsExperiment-method	XcmsExperiment
filterChromPeaks,XCMSnExp-method	XCMSnExp-filter-methods
filterColumnsIntensityAbove	filter-MChromatograms
filterColumnsIntensityAbove,MChromatograms-method	filter-MChromatograms
filterColumnsIntensityAbove,XChromatograms-method	filter-MChromatograms
filterColumnsKeepTop	filter-MChromatograms
filterColumnsKeepTop,MChromatograms-method	filter-MChromatograms
filterColumnsKeepTop,XChromatograms-method	filter-MChromatograms
filterFeatureDefinitions	XcmsExperiment
filterFeatureDefinitions,XcmsExperiment-method	XcmsExperiment
filterFeatureDefinitions,XCMSnExp-method	XCMSnExp-filter-methods
filterFeatures	filterFeatures
filterFeatures,SummarizedExperiment,BlankFlag-method	BlankFlag
filterFeatures,SummarizedExperiment,DratioFilter-method	DratioFilter
filterFeatures,SummarizedExperiment,PercentMissingFilter-method	PercentMissingFilter
filterFeatures,SummarizedExperiment,RsdFilter-method	RsdFilter
filterFeatures,XcmsResult,BlankFlag-method	BlankFlag
filterFeatures,XcmsResult,DratioFilter-method	DratioFilter
filterFeatures,XcmsResult,PercentMissingFilter-method	PercentMissingFilter
filterFeatures,XcmsResult,RsdFilter-method	RsdFilter
filterFile,MsExperiment-method	XcmsExperiment
filterFile,XcmsExperiment-method	XcmsExperiment
filterFile,XCMSnExp-method	XCMSnExp-filter-methods
FilterIntensityParam	refineChromPeaks
FilterIntensityParam-class	refineChromPeaks
filterIsolationWindow,MsExperiment-method	XcmsExperiment
filterIsolationWindow,XcmsExperiment-method	XcmsExperiment
filterMsLevel,MsExperiment-method	XcmsExperiment
filterMsLevel,XcmsExperiment-method	XcmsExperiment
filterMsLevel,XCMSnExp-method	XCMSnExp-filter-methods
filterMz,MsExperiment-method	XcmsExperiment
filterMz,XChromatogram-method	XChromatogram
filterMz,XChromatograms-method	XChromatogram
filterMz,XCMSnExp-method	XCMSnExp-filter-methods
filterMzRange,MsExperiment-method	XcmsExperiment
filterMzRange,XcmsExperiment-method	XcmsExperiment
filterRt,MsExperiment-method	XcmsExperiment
filterRt,XChromatogram-method	XChromatogram
filterRt,XChromatograms-method	XChromatogram
filterRt,XcmsExperiment-method	XcmsExperiment
filterRt,XCMSnExp-method	XCMSnExp-filter-methods
filtfft	filtfft
findChromPeaks	findChromPeaks
findChromPeaks,Chromatogram,CentWaveParam-method	findChromPeaks-Chromatogram-CentWaveParam
findChromPeaks,Chromatogram,MatchedFilterParam-method	findChromPeaks-Chromatogram-MatchedFilter
findChromPeaks,MChromatograms,CentWaveParam-method	findChromPeaks-Chromatogram-CentWaveParam
findChromPeaks,MChromatograms,MatchedFilterParam-method	findChromPeaks-Chromatogram-CentWaveParam
findChromPeaks,MsExperiment,Param-method	findChromPeaks
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,XcmsExperiment,Param-method	findChromPeaks
findChromPeaks,XCMSnExp,Param-method	XCMSnExp-class
findChromPeaks-centWave	findChromPeaks-centWave
findChromPeaks-centWaveWithPredIsoROIs	findChromPeaks-centWaveWithPredIsoROIs
findChromPeaks-Chromatogram-CentWaveParam	findChromPeaks-Chromatogram-CentWaveParam
findChromPeaks-massifquant	findChromPeaks-massifquant
findChromPeaks-matchedFilter	findChromPeaks-matchedFilter
findChromPeaksIsolationWindow	findChromPeaksIsolationWindow
findChromPeaksIsolationWindow,MsExperiment-method	findChromPeaksIsolationWindow
findChromPeaksIsolationWindow,OnDiskMSnExp-method	findChromPeaksIsolationWindow
findEqualGreater	findEqualGreater
findEqualGreaterM	findEqualGreater
findEqualLess	findEqualGreater
findMZ	findMZ
findMZ,xcmsFragments-method	findMZ
findmzROI	xcmsRaw-class
findmzROI,xcmsRaw-method	xcmsRaw-class
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
fixedMz	fillChromPeaks
fixedRt	fillChromPeaks
fromFile,MsExperiment-method	XcmsExperiment
fwhm	findChromPeaks-matchedFilter
fwhm,MatchedFilterParam-method	findChromPeaks-matchedFilter
fwhm<-	findChromPeaks-matchedFilter
fwhm<-,MatchedFilterParam-method	findChromPeaks-matchedFilter
gapExtend	adjustRtime
gapExtend,ObiwarpParam-method	adjustRtime
gapExtend<-	adjustRtime
gapExtend<-,ObiwarpParam-method	adjustRtime
gapInit	adjustRtime
gapInit,ObiwarpParam-method	adjustRtime
gapInit<-	adjustRtime
gapInit<-,ObiwarpParam-method	adjustRtime
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,XChromatograms,PeakDensityParam-method	XChromatogram
groupChromPeaks,XcmsExperiment,Param-method	groupChromPeaks
groupChromPeaks,XCMSnExp,MzClustParam-method	groupChromPeaks
groupChromPeaks,XCMSnExp,NearestPeaksParam-method	groupChromPeaks
groupChromPeaks,XCMSnExp,PeakDensityParam-method	groupChromPeaks
groupFeatures,XcmsResult,AbundanceSimilarityParam-method	groupFeatures-abundance-correlation
groupFeatures,XcmsResult,EicSimilarityParam-method	groupFeatures-eic-similarity
groupFeatures,XcmsResult,SimilarRtimeParam-method	groupFeatures-similar-rtime
groupFeatures-abundance-correlation	groupFeatures-abundance-correlation
groupFeatures-eic-similarity	groupFeatures-eic-similarity
groupFeatures-similar-rtime	groupFeatures-similar-rtime
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
groupOverlaps	groupOverlaps
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,MsExperiment-method	XcmsExperiment
hasAdjustedRtime,MsFeatureData-method	XCMSnExp-class
hasAdjustedRtime,OnDiskMSnExp-method	XCMSnExp-class
hasAdjustedRtime,XCMSnExp-method	XCMSnExp-class
hasChromPeaks	XCMSnExp-class
hasChromPeaks,MsFeatureData-method	XCMSnExp-class
hasChromPeaks,XChromatogram-method	XChromatogram
hasChromPeaks,XChromatograms-method	XChromatogram
hasChromPeaks,XcmsExperiment-method	XcmsExperiment
hasChromPeaks,XCMSnExp-method	XCMSnExp-class
hasFeatures	XCMSnExp-class
hasFeatures,MsFeatureData-method	XCMSnExp-class
hasFeatures,XChromatograms-method	XChromatogram
hasFeatures,XcmsExperiment-method	XcmsExperiment
hasFeatures,XCMSnExp-method	XCMSnExp-class
hasFilledChromPeaks	XCMSnExp-class
hasFilledChromPeaks,XChromatograms-method	XChromatogram
hasFilledChromPeaks,XcmsExperiment-method	XcmsExperiment
hasFilledChromPeaks,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
imputeRowMin	imputeRowMin
imputeRowMinRand	imputeRowMinRand
index	findChromPeaks-matchedFilter
index,MatchedFilterParam-method	findChromPeaks-matchedFilter
index<-	findChromPeaks-matchedFilter
index<-,MatchedFilterParam-method	findChromPeaks-matchedFilter
initPenalty	adjustRtime
initPenalty,ObiwarpParam-method	adjustRtime
initPenalty<-	adjustRtime
initPenalty<-,ObiwarpParam-method	adjustRtime
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
isolationWindowTargetMz	isolationWindowTargetMz-OnDiskMSnExp-method
isolationWindowTargetMz,OnDiskMSnExp-method	isolationWindowTargetMz-OnDiskMSnExp-method
kNN	groupChromPeaks
kNN,NearestPeaksParam-method	groupChromPeaks
kNN<-	groupChromPeaks
kNN<-,NearestPeaksParam-method	groupChromPeaks
LamaParama	LamaParama
LamaParama-class	LamaParama
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
loadXcmsData	loadXcmsData
localAlignment	adjustRtime
localAlignment,ObiwarpParam-method	adjustRtime
localAlignment<-	adjustRtime
localAlignment<-,ObiwarpParam-method	adjustRtime
logicalMatrix	doubleMatrix
makeacqNum	stitch-methods
makeacqNum, xcmsRaw-method	stitch-methods
manualChromPeaks	manualChromPeaks
manualChromPeaks,MsExperiment-method	manualChromPeaks
manualChromPeaks,OnDiskMSnExp-method	manualChromPeaks
manualChromPeaks,XcmsExperiment-method	manualChromPeaks
manualChromPeaks,XCMSnExp-method	manualChromPeaks
manualFeatures	manualChromPeaks
manualFeatures,XcmsExperiment-method	manualChromPeaks
manualFeatures,XCMSnExp-method	manualChromPeaks
massifquant	findChromPeaks-massifquant
MassifquantParam	findChromPeaks-massifquant
MassifquantParam-class	findChromPeaks-massifquant
matchedFilter	findChromPeaks-matchedFilter
MatchedFilterParam	findChromPeaks-matchedFilter
MatchedFilterParam-class	findChromPeaks-matchedFilter
matchedRtimes	LamaParama
matchLamasChromPeaks	LamaParama
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
maxFeatures,PeakDensityParam-method	groupChromPeaks
maxFeatures<-	groupChromPeaks
maxFeatures<-,PeakDensityParam-method	groupChromPeaks
maxIso	findChromPeaks-centWaveWithPredIsoROIs
maxIso,CentWavePredIsoParam-method	findChromPeaks-centWaveWithPredIsoROIs
maxIso<-	findChromPeaks-centWaveWithPredIsoROIs
maxIso<-,CentWavePredIsoParam-method	findChromPeaks-centWaveWithPredIsoROIs
medianFilter	medianFilter
MergeNeighboringPeaksParam	refineChromPeaks
MergeNeighboringPeaksParam-class	refineChromPeaks
minFraction	groupChromPeaks
minFraction,MzClustParam-method	groupChromPeaks
minFraction,PeakDensityParam-method	groupChromPeaks
minFraction,PeakGroupsParam-method	adjustRtime
minFraction<-	groupChromPeaks
minFraction<-,MzClustParam-method	groupChromPeaks
minFraction<-,PeakDensityParam-method	groupChromPeaks
minFraction<-,PeakGroupsParam-method	adjustRtime
minNoiseLevel	findPeaks-MSW
minNoiseLevel,MSWParam-method	findPeaks-MSW
minNoiseLevel<-	findPeaks-MSW
minNoiseLevel<-,MSWParam-method	findPeaks-MSW
minSamples	groupChromPeaks
minSamples,MzClustParam-method	groupChromPeaks
minSamples,PeakDensityParam-method	groupChromPeaks
minSamples<-	groupChromPeaks
minSamples<-,MzClustParam-method	groupChromPeaks
minSamples<-,PeakDensityParam-method	groupChromPeaks
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
MzClustParam-class	groupChromPeaks
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
mzVsRtBalance,NearestPeaksParam-method	groupChromPeaks
mzVsRtBalance<-	groupChromPeaks
mzVsRtBalance<-,NearestPeaksParam-method	groupChromPeaks
na.flatfill	na.flatfill
nearbyPeak	findPeaks-MSW
nearbyPeak,MSWParam-method	findPeaks-MSW
nearbyPeak<-	findPeaks-MSW
nearbyPeak<-,MSWParam-method	findPeaks-MSW
NearestPeaksParam	groupChromPeaks
NearestPeaksParam-class	groupChromPeaks
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
ObiwarpParam-class	adjustRtime
overlappingFeatures	overlappingFeatures
panel.cor	panel.cor
Param	GenericParam
Param-class	GenericParam
PeakDensityParam	groupChromPeaks
PeakDensityParam-class	groupChromPeaks
peakGroupsMatrix	adjustRtime
peakGroupsMatrix,PeakGroupsParam-method	adjustRtime
peakGroupsMatrix<-	adjustRtime
peakGroupsMatrix<-,PeakGroupsParam-method	adjustRtime
PeakGroupsParam	adjustRtime
PeakGroupsParam-class	adjustRtime
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
peaksWithCentWave	peaksWithCentWave
peaksWithMatchedFilter	peaksWithMatchedFilter
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
PercentMissingFilter	PercentMissingFilter
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,LamaParama,ANY-method	LamaParama
plot,MsExperiment,missing-method	XcmsExperiment
plot,XChromatogram,ANY-method	XChromatogram
plot,XChromatograms,ANY-method	XChromatogram
plot,XCMSnExp,missing-method	XCMSnExp-class
plot.xcmsEIC	plot.xcmsEIC
plotAdjustedRtime	plotAdjustedRtime
plotChrom	plotChrom-methods
plotChrom,xcmsRaw-method	plotChrom-methods
plotChromatogramsOverlay	plotChromatogramsOverlay
plotChromatogramsOverlay,MChromatograms-method	plotChromatogramsOverlay
plotChromatogramsOverlay,XChromatograms-method	plotChromatogramsOverlay
plotChromPeakDensity	plotChromPeakDensity
plotChromPeakDensity,XChromatograms-method	XChromatogram
plotChromPeakDensity,XCMSnExp-method	plotChromPeakDensity
plotChromPeakImage	plotChromPeaks
plotChromPeaks	plotChromPeaks
plotEIC	plotEIC-methods
plotEIC,xcmsRaw-method	plotEIC-methods
plotFeatureGroups	plotFeatureGroups
plotMsData	plotMsData
plotPeaks	plotPeaks-methods
plotPeaks,xcmsRaw-method	plotPeaks-methods
plotPrecursorIons	plotPrecursorIons
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,MsExperiment-method	XcmsExperiment
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
ppm,PeakDensityParam-method	groupChromPeaks
ppm<-	findChromPeaks-centWave
ppm<-,CentWaveParam-method	findChromPeaks-centWave
ppm<-,FillChromPeaksParam-method	fillChromPeaks
ppm<-,MassifquantParam-method	findChromPeaks-massifquant
ppm<-,MzClustParam-method	groupChromPeaks
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,XChromatograms-method	XChromatogram
processHistory,XcmsExperiment-method	XcmsExperiment
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,MsExperiment-method	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
quantify,XcmsExperiment-method	XcmsExperiment
quantify,XCMSnExp-method	XCMSnExp-peak-grouping-results
rawEIC	rawEIC-methods
rawEIC,xcmsRaw-method	rawEIC-methods
rawMat	rawMat-methods
rawMat,xcmsRaw-method	rawMat-methods
rawMat-methods	rawMat-methods
reconstructChromPeakSpectra	reconstructChromPeakSpectra
reconstructChromPeakSpectra,XcmsExperiment-method	reconstructChromPeakSpectra
reconstructChromPeakSpectra,XCMSnExp-method	reconstructChromPeakSpectra
rectUnique	rectUnique
refineChromPeaks	refineChromPeaks
refineChromPeaks,XChromatogram,MergeNeighboringPeaksParam-method	XChromatogram
refineChromPeaks,XChromatograms,MergeNeighboringPeaksParam-method	XChromatogram
refineChromPeaks,XcmsExperiment,CleanPeaksParam-method	refineChromPeaks
refineChromPeaks,XcmsExperiment,FilterIntensityParam-method	refineChromPeaks
refineChromPeaks,XcmsExperiment,MergeNeighboringPeaksParam-method	refineChromPeaks
refineChromPeaks,XCMSnExp,CleanPeaksParam-method	refineChromPeaks
refineChromPeaks,XCMSnExp,FilterIntensityParam-method	refineChromPeaks
refineChromPeaks,XCMSnExp,MergeNeighboringPeaksParam-method	refineChromPeaks
removeIntensity	removeIntensity-Chromatogram
removeIntensity,Chromatogram-method	removeIntensity-Chromatogram
removeIntensity,MChromatograms-method	removeIntensity-Chromatogram
removeIntensity,XChromatogram-method	removeIntensity-Chromatogram
removePeaks,XCMSnExp-method	XCMSnExp-inherited-methods
response	adjustRtime
response,ObiwarpParam-method	adjustRtime
response<-	adjustRtime
response<-,ObiwarpParam-method	adjustRtime
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
rla	rla
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
rowRla	rla
RsdFilter	RsdFilter
rtime,MsExperiment-method	XcmsExperiment
rtime,XcmsExperiment-method	XcmsExperiment
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
sampleGroups,MzClustParam-method	groupChromPeaks
sampleGroups,NearestPeaksParam-method	groupChromPeaks
sampleGroups,PeakDensityParam-method	groupChromPeaks
sampleGroups<-	groupChromPeaks
sampleGroups<-,MzClustParam-method	groupChromPeaks
sampleGroups<-,NearestPeaksParam-method	groupChromPeaks
sampleGroups<-,PeakDensityParam-method	groupChromPeaks
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,CleanPeaksParam-method	refineChromPeaks
show,FilterIntensityParam-method	refineChromPeaks
show,MergeNeighboringPeaksParam-method	refineChromPeaks
show,MsFeatureData-method	XCMSnExp-class
show,ProcessHistory-method	ProcessHistory-class
show,XChromatogram-method	XChromatogram
show,XChromatograms-method	XChromatogram
show,xcmsEIC-method	xcmsEIC-class
show,XcmsExperiment-method	XcmsExperiment
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
smooth,PeakGroupsParam-method	adjustRtime
smooth,XCMSnExp-method	XCMSnExp-inherited-methods
smooth<-	adjustRtime
smooth<-,PeakGroupsParam-method	adjustRtime
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
span,PeakGroupsParam-method	adjustRtime
span<-	adjustRtime
span<-,PeakGroupsParam-method	adjustRtime
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	adjustRtime
subset,ObiwarpParam-method	adjustRtime
subset,PeakGroupsParam-method	adjustRtime
subset-xcmsRaw	sub-xcmsRaw-logicalOrNumeric-missing-missing-method
subset<-	adjustRtime
subset<-,ObiwarpParam-method	adjustRtime
subset<-,PeakGroupsParam-method	adjustRtime
subsetAdjust	adjustRtime
subsetAdjust,ObiwarpParam-method	adjustRtime
subsetAdjust,PeakGroupsParam-method	adjustRtime
subsetAdjust<-	adjustRtime
subsetAdjust<-,ObiwarpParam-method	adjustRtime
subsetAdjust<-,PeakGroupsParam-method	adjustRtime
summarizeLamaMatch	LamaParama
transformIntensity,XChromatogram-method	XChromatogram
transformIntensity,XChromatograms-method	XChromatogram
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
uniqueMsLevels,MsExperiment-method	XcmsExperiment
updateObject,XCMSnExp-method	XCMSnExp-class
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
writeMSData,XCMSnExp,character-method	writeMSData-XCMSnExp-character-method
writeMzTab	writeMzTab
XChromatogram	XChromatogram
XChromatogram-class	XChromatogram
XChromatograms	XChromatogram
XChromatograms-class	XChromatogram
xcms-deprecated	xcms-deprecated
xcmsEIC-class	xcmsEIC-class
XcmsExperiment	XcmsExperiment
XcmsExperiment-class	XcmsExperiment
xcmsFileSource-class	xcmsFileSource-class
xcmsFragments	xcmsFragments
xcmsFragments-class	xcmsFragments-class
XCMSnExp	XCMSnExp-class
XCMSnExp-class	XCMSnExp-class
XCMSnExp-filter	XCMSnExp-filter-methods
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
xdata	loadXcmsData
xmse	loadXcmsData
XProcessHistory	ProcessHistory-class
XProcessHistory-class	ProcessHistory-class
[,XChromatograms,ANY,ANY,ANY-method	XChromatogram
[,XcmsExperiment,ANY,ANY,ANY-method	XcmsExperiment
[,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
