$,xcmsSet-method	xcmsSet-class
$<-,xcmsSet-method	xcmsSet-class
absent	absent-methods
absent,xcmsSet-method	absent-methods
absMz,MzClustParam-method	hidden_aliases
absMz,NearestPeaksParam-method	hidden_aliases
absMz<-,MzClustParam-method	hidden_aliases
absMz<-,NearestPeaksParam-method	hidden_aliases
absRt,NearestPeaksParam-method	hidden_aliases
absRt<-,NearestPeaksParam-method	hidden_aliases
addParams,MSWParam-method	hidden_aliases
addParams<-,MSWParam-method	hidden_aliases
adjustedRtime	XCMSnExp-class
adjustedRtime,MsFeatureData-method	hidden_aliases
adjustedRtime,XcmsExperiment-method	XcmsExperiment
adjustedRtime,XCMSnExp-method	XCMSnExp-class
adjustedRtime<-	XCMSnExp-class
adjustedRtime<-,MsFeatureData-method	hidden_aliases
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
adjustRtimePeakGroups,XcmsExperimentHdf5,PeakGroupsParam-method	XcmsExperimentHdf5
adjustRtimePeakGroups,XcmsResult,PeakGroupsParam-method	hidden_aliases
ampTh,MSWParam-method	hidden_aliases
ampTh<-,MSWParam-method	hidden_aliases
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,MatchedFilterParam-method	hidden_aliases
baseValue<-,MatchedFilterParam-method	hidden_aliases
BetaDistributionParam	chromPeakSummary
bin,XCMSnExp-method	XCMSnExp-inherited-methods
binSize,MatchedFilterParam-method	hidden_aliases
binSize,ObiwarpParam-method	hidden_aliases
binSize,PeakDensityParam-method	hidden_aliases
binSize<-,MatchedFilterParam-method	hidden_aliases
binSize<-,ObiwarpParam-method	adjustRtime
binSize<-,PeakDensityParam-method	hidden_aliases
binYonX	binYonX
BlankFlag	BlankFlag
breaks_on_binSize	breaks_on_binSize
breaks_on_nBins	breaks_on_nBins
bw,PeakDensityParam-method	hidden_aliases
bw<-,PeakDensityParam-method	hidden_aliases
c, c-methods	c.xcmsSet
c.XcmsExperiment	XcmsExperiment
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,ObiwarpParam-method	hidden_aliases
centerSample<-,ObiwarpParam-method	hidden_aliases
centWave	findChromPeaks-centWave
CentWaveParam	findChromPeaks-centWave
CentWaveParam-class	hidden_aliases
CentWavePredIsoParam	findChromPeaks-centWaveWithPredIsoROIs
CentWavePredIsoParam-class	hidden_aliases
centWaveWithPredIsoROIs	findChromPeaks-centWaveWithPredIsoROIs
checkBack,MassifquantParam-method	hidden_aliases
checkBack<-,MassifquantParam-method	hidden_aliases
chromatogram	chromatogram-method
chromatogram,MsExperiment-method	XcmsExperiment
chromatogram,XcmsExperiment-method	XcmsExperiment
chromatogram,XcmsExperimentHdf5-method	hidden_aliases
chromatogram,XCMSnExp-method	chromatogram-method
ChromPeakAreaParam	fillChromPeaks
ChromPeakAreaParam-class	hidden_aliases
chromPeakChromatograms	chromPeakChromatograms
chromPeakChromatograms,XcmsExperiment-method	chromPeakChromatograms
chromPeakData	XCMSnExp-class
chromPeakData,MsFeatureData-method	hidden_aliases
chromPeakData,XChromatogram-method	XChromatogram
chromPeakData,XChromatograms-method	XChromatogram
chromPeakData,XcmsExperiment-method	XcmsExperiment
chromPeakData,XcmsExperimentHdf5-method	XcmsExperimentHdf5
chromPeakData,XCMSnExp-method	XCMSnExp-class
chromPeakData<-	XCMSnExp-class
chromPeakData<-,MsFeatureData-method	hidden_aliases
chromPeakData<-,XChromatogram-method	XChromatogram
chromPeakData<-,XcmsExperiment-method	XcmsExperiment
chromPeakData<-,XcmsExperimentHdf5-method	hidden_aliases
chromPeakData<-,XCMSnExp-method	XCMSnExp-class
chromPeaks	XCMSnExp-class
chromPeaks,MsFeatureData-method	hidden_aliases
chromPeaks,XChromatogram-method	XChromatogram
chromPeaks,XChromatograms-method	XChromatogram
chromPeaks,XcmsExperiment-method	XcmsExperiment
chromPeaks,XcmsExperimentHdf5-method	hidden_aliases
chromPeaks,XCMSnExp-method	XCMSnExp-class
chromPeaks<-	XCMSnExp-class
chromPeaks<-,MsFeatureData-method	hidden_aliases
chromPeaks<-,XChromatogram-method	XChromatogram
chromPeaks<-,XcmsExperiment-method	XcmsExperiment
chromPeaks<-,XcmsExperimentHdf5-method	hidden_aliases
chromPeaks<-,XCMSnExp-method	XCMSnExp-class
chromPeakSpectra	chromPeakSpectra
chromPeakSpectra,XcmsExperiment-method	chromPeakSpectra
chromPeakSpectra,XcmsExperimentHdf5-method	hidden_aliases
chromPeakSpectra,XCMSnExp-method	chromPeakSpectra
chromPeakSummary	chromPeakSummary
chromPeakSummary,XcmsExperiment,BetaDistributionParam-method	chromPeakSummary
chromPeakSummary,XcmsExperimentHdf5,BetaDistributionParam-method	hidden_aliases
class:Param	hidden_aliases
clean,XCMSnExp-method	XCMSnExp-inherited-methods
CleanPeaksParam	refineChromPeaks
CleanPeaksParam-class	hidden_aliases
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,MassifquantParam-method	hidden_aliases
consecMissedLimit<-,MassifquantParam-method	hidden_aliases
correlate	correlate-Chromatogram
correlate,Chromatogram,Chromatogram-method	correlate-Chromatogram
correlate,MChromatograms,MChromatograms-method	correlate-Chromatogram
correlate,MChromatograms,missing-method	correlate-Chromatogram
criticalValue,MassifquantParam-method	hidden_aliases
criticalValue<-,MassifquantParam-method	hidden_aliases
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,MatchedFilterParam-method	hidden_aliases
distance<-,MatchedFilterParam-method	hidden_aliases
distFun,ObiwarpParam-method	hidden_aliases
distFun<-,ObiwarpParam-method	hidden_aliases
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	hidden_aliases
dropAdjustedRtime,XcmsExperiment-method	XcmsExperiment
dropAdjustedRtime,XcmsExperimentHdf5-method	hidden_aliases
dropAdjustedRtime,XCMSnExp-method	XCMSnExp-class
dropChromPeaks	XCMSnExp-class
dropChromPeaks,MsFeatureData-method	hidden_aliases
dropChromPeaks,XcmsExperiment-method	XcmsExperiment
dropChromPeaks,XcmsExperimentHdf5-method	hidden_aliases
dropChromPeaks,XCMSnExp-method	XCMSnExp-class
dropFeatureDefinitions	XCMSnExp-class
dropFeatureDefinitions,MsFeatureData-method	hidden_aliases
dropFeatureDefinitions,XChromatograms-method	XChromatogram
dropFeatureDefinitions,XcmsExperiment-method	XcmsExperiment
dropFeatureDefinitions,XcmsExperimentHdf5-method	hidden_aliases
dropFeatureDefinitions,XCMSnExp-method	XCMSnExp-class
dropFilledChromPeaks	XCMSnExp-class
dropFilledChromPeaks,XChromatogram-method	XChromatogram
dropFilledChromPeaks,XChromatograms-method	XChromatogram
dropFilledChromPeaks,XcmsExperiment-method	XcmsExperiment
dropFilledChromPeaks,XcmsExperimentHdf5-method	hidden_aliases
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,FillChromPeaksParam-method	hidden_aliases
expandMz<-,FillChromPeaksParam-method	hidden_aliases
expandRt,FillChromPeaksParam-method	hidden_aliases
expandRt<-,FillChromPeaksParam-method	hidden_aliases
exportMetaboAnalyst	exportMetaboAnalyst
extractMsData	extractMsData-method
extractMsData,OnDiskMSnExp-method	extractMsData-method
extractMsData,XCMSnExp-method	extractMsData-method
extraPeaks,PeakGroupsParam-method	hidden_aliases
extraPeaks<-,PeakGroupsParam-method	hidden_aliases
faahko_sub	loadXcmsData
faahko_sub2	loadXcmsData
factorDiag,ObiwarpParam-method	hidden_aliases
factorDiag<-,ObiwarpParam-method	hidden_aliases
factorGap,ObiwarpParam-method	hidden_aliases
factorGap<-,ObiwarpParam-method	hidden_aliases
family,PeakGroupsParam-method	hidden_aliases
family<-,PeakGroupsParam-method	hidden_aliases
feature-grouping	feature-grouping
featureArea	XcmsExperiment
featureArea,XcmsExperimentHdf5-method	hidden_aliases
featureArea,XcmsResult-method	XcmsExperiment
featureChromatograms	featureChromatograms
featureChromatograms,XcmsExperiment-method	featureChromatograms
featureChromatograms,XcmsExperimentHdf5-method	hidden_aliases
featureChromatograms,XCMSnExp-method	featureChromatograms
featureDefinitions	XCMSnExp-class
featureDefinitions,MsFeatureData-method	hidden_aliases
featureDefinitions,XChromatograms-method	XChromatogram
featureDefinitions,XcmsExperiment-method	XcmsExperiment
featureDefinitions,XcmsExperimentHdf5-method	hidden_aliases
featureDefinitions,XCMSnExp-method	XCMSnExp-class
featureDefinitions<-	XCMSnExp-class
featureDefinitions<-,MsFeatureData-method	hidden_aliases
featureDefinitions<-,XcmsExperiment-method	XcmsExperiment
featureDefinitions<-,XcmsExperimentHdf5-method	hidden_aliases
featureDefinitions<-,XCMSnExp-method	XCMSnExp-class
featureGroups,XcmsResult-method	feature-grouping
featureGroups<-,XcmsResult-method	feature-grouping
featureSpectra	featureSpectra
featureSpectra,XcmsExperiment-method	featureSpectra
featureSpectra,XcmsExperimentHdf5-method	hidden_aliases
featureSpectra,XCMSnExp-method	featureSpectra
featureSummary	featureSummary
featureValues	XCMSnExp-peak-grouping-results
featureValues,XChromatograms-method	XChromatogram
featureValues,XcmsExperiment-method	XcmsExperiment
featureValues,XcmsExperimentHdf5-method	hidden_aliases
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,XcmsExperimentHdf5,ChromPeakAreaParam-method	hidden_aliases
fillChromPeaks,XCMSnExp,ChromPeakAreaParam-method	fillChromPeaks
fillChromPeaks,XCMSnExp,FillChromPeaksParam-method	fillChromPeaks
fillChromPeaks,XCMSnExp,missing-method	fillChromPeaks
FillChromPeaksParam	fillChromPeaks
FillChromPeaksParam-class	hidden_aliases
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,XcmsExperimentHdf5-method	XcmsExperimentHdf5
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,XcmsExperimentHdf5-method	XcmsExperimentHdf5
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	hidden_aliases
filterIsolationWindow,MsExperiment-method	XcmsExperiment
filterIsolationWindow,XcmsExperiment-method	XcmsExperiment
filterIsolationWindow,XcmsExperimentHdf5-method	hidden_aliases
filterMsLevel,MsExperiment-method	XcmsExperiment
filterMsLevel,XcmsExperiment-method	XcmsExperiment
filterMsLevel,XcmsExperimentHdf5-method	hidden_aliases
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
filterMzRange,XcmsExperimentHdf5-method	hidden_aliases
filterRt,MsExperiment-method	XcmsExperiment
filterRt,XChromatogram-method	XChromatogram
filterRt,XChromatograms-method	XChromatogram
filterRt,XcmsExperiment-method	XcmsExperiment
filterRt,XcmsExperimentHdf5-method	hidden_aliases
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,XcmsExperimentHdf5,Param-method	hidden_aliases
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,CentWaveParam-method	hidden_aliases
firstBaselineCheck<-,CentWaveParam-method	hidden_aliases
fitgauss,CentWaveParam-method	hidden_aliases
fitgauss,MassifquantParam-method	hidden_aliases
fitgauss<-,CentWaveParam-method	hidden_aliases
fitgauss<-,MassifquantParam-method	hidden_aliases
fixedMz	hidden_aliases
fixedRt	hidden_aliases
fromFile,MsExperiment-method	XcmsExperiment
fwhm,MatchedFilterParam-method	hidden_aliases
fwhm<-,MatchedFilterParam-method	hidden_aliases
gapExtend,ObiwarpParam-method	hidden_aliases
gapExtend<-,ObiwarpParam-method	hidden_aliases
gapInit,ObiwarpParam-method	hidden_aliases
gapInit<-,ObiwarpParam-method	hidden_aliases
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,XcmsExperimentHdf5,Param-method	hidden_aliases
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	hidden_aliases
hasAdjustedRtime,OnDiskMSnExp-method	hidden_aliases
hasAdjustedRtime,XCMSnExp-method	XCMSnExp-class
hasChromPeaks	XCMSnExp-class
hasChromPeaks,MsFeatureData-method	hidden_aliases
hasChromPeaks,XChromatogram-method	XChromatogram
hasChromPeaks,XChromatograms-method	XChromatogram
hasChromPeaks,XcmsExperiment-method	XcmsExperiment
hasChromPeaks,XcmsExperimentHdf5-method	hidden_aliases
hasChromPeaks,XCMSnExp-method	XCMSnExp-class
hasFeatures	XCMSnExp-class
hasFeatures,MsFeatureData-method	hidden_aliases
hasFeatures,XChromatograms-method	XChromatogram
hasFeatures,XcmsExperiment-method	XcmsExperiment
hasFeatures,XcmsExperimentHdf5-method	hidden_aliases
hasFeatures,XCMSnExp-method	XCMSnExp-class
hasFilledChromPeaks	XCMSnExp-class
hasFilledChromPeaks,XChromatograms-method	XChromatogram
hasFilledChromPeaks,XcmsExperiment-method	XcmsExperiment
hasFilledChromPeaks,XcmsExperimentHdf5-method	hidden_aliases
hasFilledChromPeaks,XCMSnExp-method	XCMSnExp-class
hidden_aliases	hidden_aliases
highlightChromPeaks	highlightChromPeaks
image,xcmsRaw-method	image.xcmsRaw
impute,MatchedFilterParam-method	hidden_aliases
impute<-,MatchedFilterParam-method	hidden_aliases
imputeLinInterpol	imputeLinInterpol
imputeRowMin	imputeRowMin
imputeRowMinRand	imputeRowMinRand
index,MatchedFilterParam-method	hidden_aliases
index<-,MatchedFilterParam-method	hidden_aliases
initPenalty,ObiwarpParam-method	hidden_aliases
initPenalty<-,ObiwarpParam-method	hidden_aliases
integerMatrix	doubleMatrix
integrate,CentWaveParam-method	hidden_aliases
integrate,MassifquantParam-method	hidden_aliases
integrate<-,CentWaveParam-method	hidden_aliases
integrate<-,MassifquantParam-method	hidden_aliases
intensity,XCMSnExp-method	XCMSnExp-class
isCalibrated	calibrate-calibrant-mass
isolationWindowTargetMz	isolationWindowTargetMz-OnDiskMSnExp-method
isolationWindowTargetMz,OnDiskMSnExp-method	isolationWindowTargetMz-OnDiskMSnExp-method
kNN,NearestPeaksParam-method	hidden_aliases
kNN<-,NearestPeaksParam-method	hidden_aliases
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,ObiwarpParam-method	hidden_aliases
localAlignment<-,ObiwarpParam-method	hidden_aliases
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,XcmsExperimentHdf5-method	hidden_aliases
manualChromPeaks,XCMSnExp-method	manualChromPeaks
manualFeatures	manualChromPeaks
manualFeatures,XcmsExperiment-method	manualChromPeaks
manualFeatures,XcmsExperimentHdf5-method	hidden_aliases
manualFeatures,XCMSnExp-method	manualChromPeaks
massifquant	findChromPeaks-massifquant
MassifquantParam	findChromPeaks-massifquant
MassifquantParam-class	hidden_aliases
matchedFilter	findChromPeaks-matchedFilter
MatchedFilterParam	findChromPeaks-matchedFilter
MatchedFilterParam-class	hidden_aliases
matchedRtimes	LamaParama
matchLamasChromPeaks	LamaParama
max,MatchedFilterParam-method	hidden_aliases
max<-,MatchedFilterParam-method	hidden_aliases
maxCharge,CentWavePredIsoParam-method	hidden_aliases
maxCharge<-,CentWavePredIsoParam-method	hidden_aliases
maxFeatures,PeakDensityParam-method	hidden_aliases
maxFeatures<-,PeakDensityParam-method	hidden_aliases
maxIso,CentWavePredIsoParam-method	hidden_aliases
maxIso<-,CentWavePredIsoParam-method	hidden_aliases
medianFilter	medianFilter
MergeNeighboringPeaksParam	refineChromPeaks
MergeNeighboringPeaksParam-class	hidden_aliases
minFraction,MzClustParam-method	hidden_aliases
minFraction,PeakDensityParam-method	hidden_aliases
minFraction,PeakGroupsParam-method	hidden_aliases
minFraction<-,MzClustParam-method	hidden_aliases
minFraction<-,PeakDensityParam-method	hidden_aliases
minFraction<-,PeakGroupsParam-method	hidden_aliases
minNoiseLevel,MSWParam-method	hidden_aliases
minNoiseLevel<-,MSWParam-method	hidden_aliases
minSamples,MzClustParam-method	hidden_aliases
minSamples,PeakDensityParam-method	hidden_aliases
minSamples<-,MzClustParam-method	hidden_aliases
minSamples<-,PeakDensityParam-method	hidden_aliases
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	hidden_aliases
mz,CalibrantMassParam	calibrate-calibrant-mass
mz,XCMSnExp-method	XCMSnExp-class
mzCenterFun,CentWaveParam-method	hidden_aliases
mzCenterFun,MassifquantParam-method	hidden_aliases
mzCenterFun<-,CentWaveParam-method	hidden_aliases
mzCenterFun<-,MassifquantParam-method	hidden_aliases
MzClustParam	groupChromPeaks
MzClustParam-class	hidden_aliases
mzdiff,CentWaveParam-method	hidden_aliases
mzdiff,MassifquantParam-method	hidden_aliases
mzdiff,MatchedFilterParam-method	hidden_aliases
mzdiff<-,CentWaveParam-method	hidden_aliases
mzdiff<-,MassifquantParam-method	hidden_aliases
mzdiff<-,MatchedFilterParam-method	hidden_aliases
mzIntervalExtension,CentWavePredIsoParam-method	hidden_aliases
mzIntervalExtension<-,CentWavePredIsoParam-method	hidden_aliases
mzrange	xcmsEIC-class
mzrange,xcmsEIC-method	xcmsEIC-class
mzVsRtBalance,NearestPeaksParam-method	hidden_aliases
mzVsRtBalance<-,NearestPeaksParam-method	hidden_aliases
na.flatfill	na.flatfill
nearbyPeak,MSWParam-method	hidden_aliases
nearbyPeak<-,MSWParam-method	hidden_aliases
NearestPeaksParam	groupChromPeaks
NearestPeaksParam-class	hidden_aliases
noise,CentWaveParam-method	hidden_aliases
noise,MassifquantParam-method	hidden_aliases
noise<-,CentWaveParam-method	hidden_aliases
noise<-,MassifquantParam-method	hidden_aliases
normalize,XCMSnExp-method	XCMSnExp-inherited-methods
ObiwarpParam	adjustRtime
ObiwarpParam-class	hidden_aliases
overlappingFeatures	overlappingFeatures
panel.cor	panel.cor
Param	GenericParam
Param-class	hidden_aliases
PeakDensityParam	groupChromPeaks
PeakDensityParam-class	hidden_aliases
peakGroupsMatrix,PeakGroupsParam-method	hidden_aliases
peakGroupsMatrix<-,PeakGroupsParam-method	hidden_aliases
PeakGroupsParam	adjustRtime
PeakGroupsParam-class	hidden_aliases
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,MSWParam-method	hidden_aliases
peakScaleRange<-,MSWParam-method	hidden_aliases
peaksWithCentWave	peaksWithCentWave
peaksWithMatchedFilter	peaksWithMatchedFilter
peakTable	peakTable-methods
peakTable,xcmsSet-method	peakTable-methods
peakThr,MSWParam-method	hidden_aliases
peakThr<-,MSWParam-method	hidden_aliases
peakwidth,CentWaveParam-method	hidden_aliases
peakwidth,MassifquantParam-method	hidden_aliases
peakwidth<-,CentWaveParam-method	hidden_aliases
peakwidth<-,MassifquantParam-method	hidden_aliases
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	hidden_aliases
polarity,MsExperiment-method	XcmsExperiment
polarity<-,CentWavePredIsoParam-method	hidden_aliases
ppm,CentWaveParam-method	hidden_aliases
ppm,FillChromPeaksParam-method	hidden_aliases
ppm,MassifquantParam-method	hidden_aliases
ppm,MzClustParam-method	hidden_aliases
ppm,PeakDensityParam-method	hidden_aliases
ppm<-,CentWaveParam-method	hidden_aliases
ppm<-,FillChromPeaksParam-method	hidden_aliases
ppm<-,MassifquantParam-method	hidden_aliases
ppm<-,MzClustParam-method	hidden_aliases
prefilter,CentWaveParam-method	hidden_aliases
prefilter,MassifquantParam-method	hidden_aliases
prefilter<-,CentWaveParam-method	hidden_aliases
prefilter<-,MassifquantParam-method	hidden_aliases
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
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,XcmsExperimentHdf5,CleanPeaksParam-method	hidden_aliases
refineChromPeaks,XcmsExperimentHdf5,FilterIntensityParam-method	refineChromPeaks
refineChromPeaks,XcmsExperimentHdf5,MergeNeighboringPeaksParam-method	hidden_aliases
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,ObiwarpParam-method	hidden_aliases
response<-,ObiwarpParam-method	hidden_aliases
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,MSWParam-method	hidden_aliases
ridgeLength<-,MSWParam-method	hidden_aliases
rla	rla
roiList,CentWaveParam-method	hidden_aliases
roiList<-,CentWaveParam-method	hidden_aliases
roiScales,CentWaveParam-method	hidden_aliases
roiScales<-,CentWaveParam-method	hidden_aliases
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,MzClustParam-method	hidden_aliases
sampleGroups,NearestPeaksParam-method	hidden_aliases
sampleGroups,PeakDensityParam-method	hidden_aliases
sampleGroups<-,MzClustParam-method	hidden_aliases
sampleGroups<-,NearestPeaksParam-method	hidden_aliases
sampleGroups<-,PeakDensityParam-method	hidden_aliases
sampnames	sampnames-methods
sampnames,xcmsEIC-method	sampnames-methods
sampnames,xcmsSet-method	sampnames-methods
sampnames<-	xcmsSet-class
sampnames<-,xcmsSet-method	xcmsSet-class
scales,MSWParam-method	hidden_aliases
scales<-,MSWParam-method	hidden_aliases
scanrange	xcmsSet-class
scanrange,xcmsRaw-method	xcmsRaw-class
scanrange,xcmsSet-method	xcmsSet-class
setAs	XCMSnExp-class
show,MsFeatureData-method	hidden_aliases
show,ProcessHistory-method	hidden_aliases
show,XChromatogram-method	hidden_aliases
show,XChromatograms-method	hidden_aliases
show,xcmsEIC-method	hidden_aliases
show,XcmsExperiment-method	hidden_aliases
show,XcmsExperimentHdf5-method	hidden_aliases
show,xcmsFragments-method	hidden_aliases
show,XCMSnExp-method	hidden_aliases
show,xcmsPeaks-method	hidden_aliases
show,xcmsRaw-method	hidden_aliases
show,xcmsSet-method	hidden_aliases
show,XProcessHistory-method	hidden_aliases
showError	showError-xcmsSet-method
showError,xcmsSet-method	showError-xcmsSet-method
sigma,MatchedFilterParam-method	hidden_aliases
sigma<-,MatchedFilterParam-method	hidden_aliases
smooth,PeakGroupsParam-method	hidden_aliases
smooth,XCMSnExp-method	XCMSnExp-inherited-methods
smooth<-,PeakGroupsParam-method	hidden_aliases
snthresh,CentWaveParam-method	hidden_aliases
snthresh,MassifquantParam-method	hidden_aliases
snthresh,MatchedFilterParam-method	hidden_aliases
snthresh,MSWParam-method	hidden_aliases
snthresh<-,CentWaveParam-method	hidden_aliases
snthresh<-,MassifquantParam-method	hidden_aliases
snthresh<-,MatchedFilterParam-method	hidden_aliases
snthresh<-,MSWParam-method	hidden_aliases
snthreshIsoROIs,CentWavePredIsoParam-method	hidden_aliases
snthreshIsoROIs<-,CentWavePredIsoParam-method	hidden_aliases
sortMz	xcmsRaw-class
sortMz,xcmsRaw-method	xcmsRaw-class
span,PeakGroupsParam-method	hidden_aliases
span<-,PeakGroupsParam-method	hidden_aliases
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,MatchedFilterParam-method	hidden_aliases
steps<-,MatchedFilterParam-method	hidden_aliases
stitch	stitch-methods
stitch,xcmsRaw-method	stitch-methods
stitch-methods	stitch-methods
stitch.netCDF	stitch-methods
stitch.xml	stitch-methods
subset,ObiwarpParam-method	hidden_aliases
subset,PeakGroupsParam-method	hidden_aliases
subset-xcmsRaw	sub-xcmsRaw-logicalOrNumeric-missing-missing-method
subset<-,ObiwarpParam-method	hidden_aliases
subset<-,PeakGroupsParam-method	hidden_aliases
subsetAdjust,ObiwarpParam-method	hidden_aliases
subsetAdjust,PeakGroupsParam-method	hidden_aliases
subsetAdjust<-,ObiwarpParam-method	hidden_aliases
subsetAdjust<-,PeakGroupsParam-method	hidden_aliases
summarizeLamaMatch	LamaParama
toXcmsExperiment	XcmsExperimentHdf5
toXcmsExperimentHdf5	XcmsExperimentHdf5
transformIntensity,XChromatogram-method	XChromatogram
transformIntensity,XChromatograms-method	XChromatogram
tuneIn,MSWParam-method	hidden_aliases
tuneIn<-,MSWParam-method	hidden_aliases
unions,MassifquantParam-method	hidden_aliases
unions<-,MassifquantParam-method	hidden_aliases
uniqueMsLevels,MsExperiment-method	XcmsExperiment
updateObject,XCMSnExp-method	XCMSnExp-class
updateObject,xcmsSet-method	updateObject-xcmsSet-method
useOriginalCode	useOriginalCode
verboseColumns,CentWaveParam-method	hidden_aliases
verboseColumns,MassifquantParam-method	hidden_aliases
verboseColumns,MSWParam-method	hidden_aliases
verboseColumns<-,CentWaveParam-method	hidden_aliases
verboseColumns<-,MassifquantParam-method	hidden_aliases
verboseColumns<-,MSWParam-method	hidden_aliases
verify.mzQuantML	verify.mzQuantML
which.colMax	colMax
which.rowMax	colMax
withWave,MassifquantParam-method	hidden_aliases
withWave<-,MassifquantParam-method	hidden_aliases
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
XcmsExperimentHdf5	XcmsExperimentHdf5
XcmsExperimentHdf5-class	XcmsExperimentHdf5
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
[,XcmsExperimentHdf5,ANY,ANY,ANY-method	hidden_aliases
[,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
