# LC/MS and GC/MS Data Analysis

## Documentation for package ‘xcms’ version 3.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P R S T U V W X misc

## -- A --

absent | Determine which peaks are absent / present in a sample class
absent-method | Determine which peaks are absent / present in a sample class
absMz | High resolution peak grouping for single spectra samples
absMz-method | High resolution peak grouping for single spectra samples
absMz-method | Peak grouping based on proximity in the mz-rt space
absMz<- | High resolution peak grouping for single spectra samples
absMz<--method | High resolution peak grouping for single spectra samples
absMz<--method | Peak grouping based on proximity in the mz-rt space
absRt | Peak grouping based on proximity in the mz-rt space
absRt-method | Peak grouping based on proximity in the mz-rt space
absRt<- | Peak grouping based on proximity in the mz-rt space
absRt<--method | Peak grouping based on proximity in the mz-rt space
addParams | Single-spectrum non-chromatography MS data peak detection
addParams-method | Single-spectrum non-chromatography MS data peak detection
addParams<- | Single-spectrum non-chromatography MS data peak detection
addParams<--method | Single-spectrum non-chromatography MS data peak detection
adjustedRtime | Data container storing xcms preprocessing results
adjustedRtime-method | Data container storing xcms preprocessing results
adjustedRtime<- | Data container storing xcms preprocessing results
adjustedRtime<--method | Data container storing xcms preprocessing results
adjustRtime | Alignment: Retention time correction methods.
adjustRtime-method | Align retention times across samples using Obiwarp
adjustRtime-method | Retention time correction based on alignment of house keeping peak groups
adjustRtime-obiwarp | Align retention times across samples using Obiwarp
adjustRtime-peakGroups | Retention time correction based on alignment of house keeping peak groups
adjustRtimePeakGroups | Retention time correction based on alignment of house keeping peak groups
ampTh | Single-spectrum non-chromatography MS data peak detection
ampTh-method | Single-spectrum non-chromatography MS data peak detection
ampTh<- | Single-spectrum non-chromatography MS data peak detection
ampTh<--method | Single-spectrum non-chromatography MS data peak detection
applyAdjustedRtime | Replace raw with adjusted retention times
AutoLockMass | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~
AutoLockMass-method | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~
AutoLockMass-methods | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~

## -- B --

baseValue | Peak detection in the chromatographic time domain
baseValue-method | Peak detection in the chromatographic time domain
baseValue<- | Peak detection in the chromatographic time domain
baseValue<--method | Peak detection in the chromatographic time domain
bin-method | XCMSnExp data manipulation methods inherited from MSnbase
binSize | Peak detection in the chromatographic time domain
binSize-method | Align retention times across samples using Obiwarp
binSize-method | Peak detection in the chromatographic time domain
binSize-method | Peak grouping based on time dimension peak densities
binSize<- | Peak detection in the chromatographic time domain
binSize<--method | Align retention times across samples using Obiwarp
binSize<--method | Peak detection in the chromatographic time domain
binSize<--method | Peak grouping based on time dimension peak densities
binYonX | Aggregate values in y for bins defined on x
breaks_on_binSize | Generate breaks for binning using a defined bin size.
breaks_on_nBins | Generate breaks for binning
bw | Peak grouping based on time dimension peak densities
bw-method | Peak grouping based on time dimension peak densities
bw<- | Peak grouping based on time dimension peak densities
bw<--method | Peak grouping based on time dimension peak densities

## -- C --

c, c-methods | Combine xcmsSet objects
c.xcmsSet | Combine xcmsSet objects
CalibrantMassParam | Calibrant mass based calibration of chromatgraphic peaks
CalibrantMassParam-class | Calibrant mass based calibration of chromatgraphic peaks
calibrate | Calibrate peaks for correcting unprecise m/z values
calibrate-method | Calibrant mass based calibration of chromatgraphic peaks
calibrate-method | Calibrate peaks for correcting unprecise m/z values
centerSample | Align retention times across samples using Obiwarp
centerSample-method | Align retention times across samples using Obiwarp
centerSample<- | Align retention times across samples using Obiwarp
centerSample<--method | Align retention times across samples using Obiwarp
centWave | Chromatographic peak detection using the centWave method
CentWaveParam | Chromatographic peak detection using the centWave method
CentWaveParam-class | Chromatographic peak detection using the centWave method
CentWavePredIsoParam | Two-step centWave peak detection considering also isotopes
CentWavePredIsoParam-class | Two-step centWave peak detection considering also isotopes
centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes
checkBack | Chromatographic peak detection using the massifquant method
checkBack-method | Chromatographic peak detection using the massifquant method
checkBack<- | Chromatographic peak detection using the massifquant method
checkBack<--method | Chromatographic peak detection using the massifquant method
chromatogram | Extracting chromatograms
chromatogram-method | Extracting chromatograms
chromatographic-peak-detection | Chromatographic peak detection methods.
chromPeaks | Data container storing xcms preprocessing results
chromPeaks-method | Data container storing xcms preprocessing results
chromPeaks<- | Data container storing xcms preprocessing results
chromPeaks<--method | Data container storing xcms preprocessing results
clean-method | XCMSnExp data manipulation methods inherited from MSnbase
collect | Collect MS^n peaks into xcmsFragments
collect-method | Collect MS^n peaks into xcmsFragments
collect-methods | Collect MS^n peaks into xcmsFragments
consecMissedLimit | Chromatographic peak detection using the massifquant method
consecMissedLimit-method | Chromatographic peak detection using the massifquant method
consecMissedLimit<- | Chromatographic peak detection using the massifquant method
consecMissedLimit<--method | Chromatographic peak detection using the massifquant method
criticalValue | Chromatographic peak detection using the massifquant method
criticalValue-method | Chromatographic peak detection using the massifquant method
criticalValue<- | Chromatographic peak detection using the massifquant method
criticalValue<--method | Chromatographic peak detection using the massifquant method

## -- D --

deepCopy | Constructor for xcmsRaw objects which reads NetCDF/mzXML files
deepCopy-method | Constructor for xcmsRaw objects which reads NetCDF/mzXML files
diffreport | Create report of analyte differences
diffreport-method | Create report of analyte differences
distance | Peak detection in the chromatographic time domain
distance-method | Peak detection in the chromatographic time domain
distance<- | Peak detection in the chromatographic time domain
distance<--method | Peak detection in the chromatographic time domain
distFun | Align retention times across samples using Obiwarp
distFun-method | Align retention times across samples using Obiwarp
distFun<- | Align retention times across samples using Obiwarp
distFun<--method | Align retention times across samples using Obiwarp
do_adjustRtime_peakGroups | Align spectrum retention times across samples using peak groups found in most samples
do_findChromPeaks_addPredIsoROIs | Core API function for two-step centWave peak detection with isotopes
do_findChromPeaks_centWave | Core API function for centWave peak detection
do_findChromPeaks_centWaveWithPredIsoROIs | Core API function for two-step centWave peak detection with isotopes
do_findChromPeaks_massifquant | Core API function for massifquant peak detection
do_findChromPeaks_matchedFilter | Core API function for matchedFilter peak detection
do_findPeaks_MSW | Core API function for single-spectrum non-chromatography MS data peak detection
do_groupChromPeaks_density | Core API function for peak density based chromatographic peak grouping
do_groupChromPeaks_nearest | Core API function for chromatic peak grouping using a nearest neighbor approach
do_groupPeaks_mzClust | Core API function for peak grouping using mzClust
dropAdjustedRtime | Data container storing xcms preprocessing results
dropAdjustedRtime-method | Data container storing xcms preprocessing results
dropChromPeaks | Data container storing xcms preprocessing results
dropChromPeaks-method | Data container storing xcms preprocessing results
dropFeatureDefinitions | Data container storing xcms preprocessing results
dropFeatureDefinitions-method | Data container storing xcms preprocessing results
dropFilledChromPeaks | Data container storing xcms preprocessing results
dropFilledChromPeaks-method | Data container storing xcms preprocessing results

## -- E --

etg | Empirically Transformed Gaussian function
expandMz | Integrate areas of missing peaks
expandMz-method | Integrate areas of missing peaks
expandMz<- | Integrate areas of missing peaks
expandMz<--method | Integrate areas of missing peaks
expandRt | Integrate areas of missing peaks
expandRt-method | Integrate areas of missing peaks
expandRt<- | Integrate areas of missing peaks
expandRt<--method | Integrate areas of missing peaks
extractChromatograms | Deprecated functions in package 'xcms'
extractChromatograms-method | Deprecated functions in package 'xcms'
extractMsData | Extract a 'data.frame' containing MS data
extractMsData-method | Extract a 'data.frame' containing MS data
extraPeaks | Retention time correction based on alignment of house keeping peak groups
extraPeaks-method | Retention time correction based on alignment of house keeping peak groups
extraPeaks<- | Retention time correction based on alignment of house keeping peak groups
extraPeaks<--method | Retention time correction based on alignment of house keeping peak groups

## -- F --

factorDiag | Align retention times across samples using Obiwarp
factorDiag-method | Align retention times across samples using Obiwarp
factorDiag<- | Align retention times across samples using Obiwarp
factorDiag<--method | Align retention times across samples using Obiwarp
factorGap | Align retention times across samples using Obiwarp
factorGap-method | Align retention times across samples using Obiwarp
factorGap<- | Align retention times across samples using Obiwarp
factorGap<--method | Align retention times across samples using Obiwarp
family | Retention time correction based on alignment of house keeping peak groups
family-method | Retention time correction based on alignment of house keeping peak groups
family<- | Retention time correction based on alignment of house keeping peak groups
family<--method | Retention time correction based on alignment of house keeping peak groups
featureDefinitions | Data container storing xcms preprocessing results
featureDefinitions-method | Data container storing xcms preprocessing results
featureDefinitions<- | Data container storing xcms preprocessing results
featureDefinitions<--method | Data container storing xcms preprocessing results
featureValues | Accessing mz-rt feature data values
featureValues-method | Accessing mz-rt feature data values
fileIndex | Tracking data processing
fileIndex-method | Tracking data processing
filepaths | Class xcmsSet, a class for preprocessing peak data
filepaths-method | Class xcmsSet, a class for preprocessing peak data
filepaths<- | Class xcmsSet, a class for preprocessing peak data
filepaths<--method | Class xcmsSet, a class for preprocessing peak data
fillChromPeaks | Integrate areas of missing peaks
fillChromPeaks-method | Integrate areas of missing peaks
FillChromPeaksParam | Integrate areas of missing peaks
FillChromPeaksParam-class | Integrate areas of missing peaks
fillPeaks | Integrate areas of missing peaks
fillPeaks-method | Integrate areas of missing peaks
fillPeaks.chrom | Integrate areas of missing peaks
fillPeaks.chrom-method | Integrate areas of missing peaks
fillPeaks.MSW | Integrate areas of missing peaks in FTICR-MS data
fillPeaks.MSW-method | Integrate areas of missing peaks in FTICR-MS data
filterAcquisitionNum-method | XCMSnExp data manipulation methods inherited from MSnbase
filterFile-method | XCMSnExp filtering and subsetting
filterMsLevel-method | XCMSnExp filtering and subsetting
filterMz-method | XCMSnExp filtering and subsetting
filterRt-method | XCMSnExp filtering and subsetting
findChromPeaks | Chromatographic peak detection methods.
findChromPeaks-centWave | Chromatographic peak detection using the centWave method
findChromPeaks-centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes
findChromPeaks-massifquant | Chromatographic peak detection using the massifquant method
findChromPeaks-matchedFilter | Peak detection in the chromatographic time domain
findChromPeaks-method | Data container storing xcms preprocessing results
findChromPeaks-method | Chromatographic peak detection using the centWave method
findChromPeaks-method | Two-step centWave peak detection considering also isotopes
findChromPeaks-method | Chromatographic peak detection using the massifquant method
findChromPeaks-method | Peak detection in the chromatographic time domain
findChromPeaks-method | Single-spectrum non-chromatography MS data peak detection
findMZ | Find fragment ions in xcmsFragment objects
findMZ-method | Find fragment ions in xcmsFragment objects
findneutral | Find neutral losses in xcmsFragment objects
findneutral-method | Find neutral losses in xcmsFragment objects
findPeaks | Feature detection for GC/MS and LC/MS Data - methods
findPeaks-method | Feature detection for GC/MS and LC/MS Data - methods
findPeaks-methods | Feature detection for GC/MS and LC/MS Data - methods
findPeaks-MSW | Single-spectrum non-chromatography MS data peak detection
findPeaks.addPredictedIsotopeFeatures | Feature detection based on predicted isotope features for high resolution LC/MS data
findPeaks.addPredictedIsotopeFeatures-method | Feature detection based on predicted isotope features for high resolution LC/MS data
findPeaks.centWave | Feature detection for high resolution LC/MS data
findPeaks.centWave-method | Feature detection for high resolution LC/MS data
findPeaks.centWaveWithPredictedIsotopeROIs | Feature detection with centWave and additional isotope features
findPeaks.centWaveWithPredictedIsotopeROIs-method | Feature detection with centWave and additional isotope features
findPeaks.massifquant | Feature detection for XC-MS data.
findPeaks.massifquant-method | Feature detection for XC-MS data.
findPeaks.matchedFilter | Peak detection in the chromatographic time domain
findPeaks.matchedFilter-method | Peak detection in the chromatographic time domain
findPeaks.MS1 | Collecting MS1 precursor peaks
findPeaks.MS1-method | Collecting MS1 precursor peaks
findPeaks.MSW | Peak detection for single-spectrum non-chromatography MS data
findPeaks.MSW-method | Peak detection for single-spectrum non-chromatography MS data
firstBaselineCheck | Chromatographic peak detection using the centWave method
firstBaselineCheck-method | Chromatographic peak detection using the centWave method
firstBaselineCheck<- | Chromatographic peak detection using the centWave method
firstBaselineCheck<--method | Chromatographic peak detection using the centWave method
fitgauss | Chromatographic peak detection using the centWave method
fitgauss-method | Chromatographic peak detection using the centWave method
fitgauss-method | Chromatographic peak detection using the massifquant method
fitgauss<- | Chromatographic peak detection using the centWave method
fitgauss<--method | Chromatographic peak detection using the centWave method
fitgauss<--method | Chromatographic peak detection using the massifquant method
fwhm | Peak detection in the chromatographic time domain
fwhm-method | Peak detection in the chromatographic time domain
fwhm<- | Peak detection in the chromatographic time domain
fwhm<--method | Peak detection in the chromatographic time domain

## -- G --

gapExtend | Align retention times across samples using Obiwarp
gapExtend-method | Align retention times across samples using Obiwarp
gapExtend<- | Align retention times across samples using Obiwarp
gapExtend<--method | Align retention times across samples using Obiwarp
gapInit | Align retention times across samples using Obiwarp
gapInit-method | Align retention times across samples using Obiwarp
gapInit<- | Align retention times across samples using Obiwarp
gapInit<--method | Align retention times across samples using Obiwarp
GenericParam | Generic parameter class
GenericParam-class | Generic parameter class
getEIC | Get extracted ion chromatograms for specified m/z ranges
getEIC-method | Get extracted ion chromatograms for specified m/z ranges
getMsnScan | Get m/z and intensity values for a single mass scan
getMsnScan-method | Get m/z and intensity values for a single mass scan
getPeaks | Get peak intensities for specified regions
getPeaks-method | Get peak intensities for specified regions
getScan | Get m/z and intensity values for a single mass scan
getScan-method | Get m/z and intensity values for a single mass scan
getSpec | Get average m/z and intensity values for multiple mass scans
getSpec-method | Get average m/z and intensity values for multiple mass scans
getXcmsRaw | Load the raw data for one or more files in the xcmsSet
getXcmsRaw-method | Load the raw data for one or more files in the xcmsSet
group | Group peaks from different samples together
group-method | Group peaks from different samples together
group-methods | Group peaks from different samples together
group.density | Group peaks from different samples together
group.density-method | Group peaks from different samples together
group.mzClust | Group Peaks via High Resolution Alignment
group.mzClust-method | Group Peaks via High Resolution Alignment
group.nearest | Group peaks from different samples together
group.nearest-method | Group peaks from different samples together
groupChromPeaks | Correspondence: Chromatographic peak grouping methods.
groupChromPeaks-density | Peak grouping based on time dimension peak densities
groupChromPeaks-method | Peak grouping based on time dimension peak densities
groupChromPeaks-method | High resolution peak grouping for single spectra samples
groupChromPeaks-method | Peak grouping based on proximity in the mz-rt space
groupChromPeaks-mzClust | High resolution peak grouping for single spectra samples
groupChromPeaks-nearest | Peak grouping based on proximity in the mz-rt space
groupidx | Class xcmsSet, a class for preprocessing peak data
groupidx-method | Class xcmsSet, a class for preprocessing peak data
groupidx<- | Class xcmsSet, a class for preprocessing peak data
groupidx<--method | Class xcmsSet, a class for preprocessing peak data
groupnames | Generate unque names for peak groups
groupnames-method | Generate unque names for peak groups
groups | Class xcmsSet, a class for preprocessing peak data
groups-method | Class xcmsSet, a class for preprocessing peak data
groups<- | Class xcmsSet, a class for preprocessing peak data
groups<--method | Class xcmsSet, a class for preprocessing peak data
groupval | Extract a matrix of peak values for each group
groupval-method | Extract a matrix of peak values for each group

## -- H --

hasAdjustedRtime | Data container storing xcms preprocessing results
hasAdjustedRtime-method | Data container storing xcms preprocessing results
hasChromPeaks | Data container storing xcms preprocessing results
hasChromPeaks-method | Data container storing xcms preprocessing results
hasFeatures | Data container storing xcms preprocessing results
hasFeatures-method | Data container storing xcms preprocessing results
highlightChromPeaks | Add definition of chromatographic peaks to an extracted chromatogram plot

## -- I --

image-method | Plot log intensity image of a xcmsRaw object
impute-method | Peak detection in the chromatographic time domain
impute<- | Peak detection in the chromatographic time domain
impute<--method | Peak detection in the chromatographic time domain
imputeLinInterpol | Impute values for empty elements in a vector using linear interpolation
index | Peak detection in the chromatographic time domain
index-method | Peak detection in the chromatographic time domain
index<- | Peak detection in the chromatographic time domain
index<--method | Peak detection in the chromatographic time domain
initPenalty | Align retention times across samples using Obiwarp
initPenalty-method | Align retention times across samples using Obiwarp
initPenalty<- | Align retention times across samples using Obiwarp
initPenalty<--method | Align retention times across samples using Obiwarp
integrate-method | Chromatographic peak detection using the centWave method
integrate-method | Chromatographic peak detection using the massifquant method
integrate<- | Chromatographic peak detection using the centWave method
integrate<--method | Chromatographic peak detection using the centWave method
integrate<--method | Chromatographic peak detection using the massifquant method
intensity-method | Data container storing xcms preprocessing results
isCalibrated | Calibrant mass based calibration of chromatgraphic peaks

## -- K --

kNN | Peak grouping based on proximity in the mz-rt space
kNN-method | Peak grouping based on proximity in the mz-rt space
kNN<- | Peak grouping based on proximity in the mz-rt space
kNN<--method | Peak grouping based on proximity in the mz-rt space

## -- L --

levelplot | Class xcmsRaw, a class for handling raw data
levelplot-method | Plot log intensity image of a xcmsRaw object
loadRaw | Read binary data from a source
loadRaw-method | Read binary data from a source
loadRaw-methods | Read binary data from a source
localAlignment | Align retention times across samples using Obiwarp
localAlignment-method | Align retention times across samples using Obiwarp
localAlignment<- | Align retention times across samples using Obiwarp
localAlignment<--method | Align retention times across samples using Obiwarp

## -- M --

makeacqNum | Correct gaps in data
makeacqNum-method | Correct gaps in data
massifquant | Chromatographic peak detection using the massifquant method
MassifquantParam | Chromatographic peak detection using the massifquant method
MassifquantParam-class | Chromatographic peak detection using the massifquant method
matchedFilter | Peak detection in the chromatographic time domain
MatchedFilterParam | Peak detection in the chromatographic time domain
MatchedFilterParam-class | Peak detection in the chromatographic time domain
max-method | Peak detection in the chromatographic time domain
max<- | Peak detection in the chromatographic time domain
max<--method | Peak detection in the chromatographic time domain
maxCharge | Two-step centWave peak detection considering also isotopes
maxCharge-method | Two-step centWave peak detection considering also isotopes
maxCharge<- | Two-step centWave peak detection considering also isotopes
maxCharge<--method | Two-step centWave peak detection considering also isotopes
maxFeatures | Peak grouping based on time dimension peak densities
maxFeatures-method | Peak grouping based on time dimension peak densities
maxFeatures<- | Peak grouping based on time dimension peak densities
maxFeatures<--method | Peak grouping based on time dimension peak densities
maxIso | Two-step centWave peak detection considering also isotopes
maxIso-method | Two-step centWave peak detection considering also isotopes
maxIso<- | Two-step centWave peak detection considering also isotopes
maxIso<--method | Two-step centWave peak detection considering also isotopes
medianFilter | Apply a median filter to a matrix
minFraction | Peak grouping based on time dimension peak densities
minFraction-method | Retention time correction based on alignment of house keeping peak groups
minFraction-method | Peak grouping based on time dimension peak densities
minFraction-method | High resolution peak grouping for single spectra samples
minFraction<- | Peak grouping based on time dimension peak densities
minFraction<--method | Retention time correction based on alignment of house keeping peak groups
minFraction<--method | Peak grouping based on time dimension peak densities
minFraction<--method | High resolution peak grouping for single spectra samples
minNoiseLevel | Single-spectrum non-chromatography MS data peak detection
minNoiseLevel-method | Single-spectrum non-chromatography MS data peak detection
minNoiseLevel<- | Single-spectrum non-chromatography MS data peak detection
minNoiseLevel<--method | Single-spectrum non-chromatography MS data peak detection
minSamples | Peak grouping based on time dimension peak densities
minSamples-method | Peak grouping based on time dimension peak densities
minSamples-method | High resolution peak grouping for single spectra samples
minSamples<- | Peak grouping based on time dimension peak densities
minSamples<--method | Peak grouping based on time dimension peak densities
minSamples<--method | High resolution peak grouping for single spectra samples
mslevel | Class xcmsSet, a class for preprocessing peak data
msLevel-method | Tracking data processing
mslevel-method | Class xcmsRaw, a class for handling raw data
mslevel-method | Class xcmsSet, a class for preprocessing peak data
msn2xcmsRaw | Copy MSn data in an xcmsRaw to the MS slots
MSW | Single-spectrum non-chromatography MS data peak detection
MSWParam | Single-spectrum non-chromatography MS data peak detection
MSWParam-class | Single-spectrum non-chromatography MS data peak detection
mz,CalibrantMassParam | Calibrant mass based calibration of chromatgraphic peaks
mz-method | Data container storing xcms preprocessing results
mzCenterFun | Chromatographic peak detection using the centWave method
mzCenterFun-method | Chromatographic peak detection using the centWave method
mzCenterFun-method | Chromatographic peak detection using the massifquant method
mzCenterFun<- | Chromatographic peak detection using the centWave method
mzCenterFun<--method | Chromatographic peak detection using the centWave method
mzCenterFun<--method | Chromatographic peak detection using the massifquant method
MzClustParam | High resolution peak grouping for single spectra samples
MzClustParam-class | High resolution peak grouping for single spectra samples
mzdiff | Chromatographic peak detection using the centWave method
mzdiff-method | Chromatographic peak detection using the centWave method
mzdiff-method | Chromatographic peak detection using the massifquant method
mzdiff-method | Peak detection in the chromatographic time domain
mzdiff<- | Chromatographic peak detection using the centWave method
mzdiff<--method | Chromatographic peak detection using the centWave method
mzdiff<--method | Chromatographic peak detection using the massifquant method
mzdiff<--method | Peak detection in the chromatographic time domain
mzIntervalExtension | Two-step centWave peak detection considering also isotopes
mzIntervalExtension-method | Two-step centWave peak detection considering also isotopes
mzIntervalExtension<- | Two-step centWave peak detection considering also isotopes
mzIntervalExtension<--method | Two-step centWave peak detection considering also isotopes
mzrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
mzrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
mzVsRtBalance | Peak grouping based on proximity in the mz-rt space
mzVsRtBalance-method | Peak grouping based on proximity in the mz-rt space
mzVsRtBalance<- | Peak grouping based on proximity in the mz-rt space
mzVsRtBalance<--method | Peak grouping based on proximity in the mz-rt space

## -- N --

nearbyPeak | Single-spectrum non-chromatography MS data peak detection
nearbyPeak-method | Single-spectrum non-chromatography MS data peak detection
nearbyPeak<- | Single-spectrum non-chromatography MS data peak detection
nearbyPeak<--method | Single-spectrum non-chromatography MS data peak detection
NearestPeaksParam | Peak grouping based on proximity in the mz-rt space
NearestPeaksParam-class | Peak grouping based on proximity in the mz-rt space
noise | Chromatographic peak detection using the centWave method
noise-method | Chromatographic peak detection using the centWave method
noise-method | Chromatographic peak detection using the massifquant method
noise<- | Chromatographic peak detection using the centWave method
noise<--method | Chromatographic peak detection using the centWave method
noise<--method | Chromatographic peak detection using the massifquant method
normalize-method | XCMSnExp data manipulation methods inherited from MSnbase

## -- O --

ObiwarpParam | Align retention times across samples using Obiwarp
ObiwarpParam-class | Align retention times across samples using Obiwarp

## -- P --

PeakDensityParam | Peak grouping based on time dimension peak densities
PeakDensityParam-class | Peak grouping based on time dimension peak densities
peakGroupsMatrix | Retention time correction based on alignment of house keeping peak groups
peakGroupsMatrix-method | Retention time correction based on alignment of house keeping peak groups
peakGroupsMatrix<- | Retention time correction based on alignment of house keeping peak groups
peakGroupsMatrix<--method | Retention time correction based on alignment of house keeping peak groups
PeakGroupsParam | Retention time correction based on alignment of house keeping peak groups
PeakGroupsParam-class | Retention time correction based on alignment of house keeping peak groups
peakPlots-method | Plot a grid of a large number of peaks
peakPlots-methods | Plot a grid of a large number of peaks
peaks | Class xcmsSet, a class for preprocessing peak data
peaks-method | Class xcmsSet, a class for preprocessing peak data
peaks<- | Class xcmsSet, a class for preprocessing peak data
peaks<--method | Class xcmsSet, a class for preprocessing peak data
peakScaleRange | Single-spectrum non-chromatography MS data peak detection
peakScaleRange-method | Single-spectrum non-chromatography MS data peak detection
peakScaleRange<- | Single-spectrum non-chromatography MS data peak detection
peakScaleRange<--method | Single-spectrum non-chromatography MS data peak detection
peakTable | Create report of aligned peak intensities
peakTable-method | Create report of aligned peak intensities
peakThr | Single-spectrum non-chromatography MS data peak detection
peakThr-method | Single-spectrum non-chromatography MS data peak detection
peakThr<- | Single-spectrum non-chromatography MS data peak detection
peakThr<--method | Single-spectrum non-chromatography MS data peak detection
peakwidth | Chromatographic peak detection using the centWave method
peakwidth-method | Chromatographic peak detection using the centWave method
peakwidth-method | Chromatographic peak detection using the massifquant method
peakwidth<- | Chromatographic peak detection using the centWave method
peakwidth<--method | Chromatographic peak detection using the centWave method
peakwidth<--method | Chromatographic peak detection using the massifquant method
phenoData | Class xcmsSet, a class for preprocessing peak data
phenoData-method | Class xcmsSet, a class for preprocessing peak data
phenoData<- | Class xcmsSet, a class for preprocessing peak data
phenoData<--method | Class xcmsSet, a class for preprocessing peak data
phenoDataFromPaths | Derive experimental design from file paths
pickPeaks-method | XCMSnExp data manipulation methods inherited from MSnbase
plot, plot-methods | Plot extracted ion chromatograms from multiple files
plot.xcmsEIC | Plot extracted ion chromatograms from multiple files
plotAdjustedRtime | Visualization of alignment results
plotChrom | Plot extracted ion chromatograms from the profile matrix
plotChrom-method | Plot extracted ion chromatograms from the profile matrix
plotChromatogram | Deprecated functions in package 'xcms'
plotChromPeakDensity | Plot chromatographic peak density along the retention time axis
plotChromPeakImage | General visualizations of peak detection results
plotChromPeaks | General visualizations of peak detection results
plotEIC | Plot extracted ion chromatograms for specified m/z range
plotEIC-method | Plot extracted ion chromatograms for specified m/z range
plotMsData | Create a plot that combines a XIC and a mz/rt 2D plot for one sample
plotPeaks | Plot a grid of a large number of peaks
plotPeaks-method | Plot a grid of a large number of peaks
plotQC | Plot m/z and RT deviations for QC purposes without external reference data
plotRaw | Scatterplot of raw data points
plotRaw-method | Scatterplot of raw data points
plotrt | Plot retention time deviation profiles
plotrt-method | Plot retention time deviation profiles
plotScan | Plot a single mass scan
plotScan-method | Plot a single mass scan
plotSpec | Plot mass spectra from the profile matrix
plotSpec-method | Plot mass spectra from the profile matrix
plotSurf | Plot profile matrix 3D surface using OpenGL
plotSurf-method | Plot profile matrix 3D surface using OpenGL
plotTIC | Plot total ion count
plotTIC-method | Plot total ion count
plotTree | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
plotTree-method | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
polarity-method | Two-step centWave peak detection considering also isotopes
polarity<- | Two-step centWave peak detection considering also isotopes
polarity<--method | Two-step centWave peak detection considering also isotopes
ppm | Chromatographic peak detection using the centWave method
ppm-method | Integrate areas of missing peaks
ppm-method | Chromatographic peak detection using the centWave method
ppm-method | Chromatographic peak detection using the massifquant method
ppm-method | High resolution peak grouping for single spectra samples
ppm<- | Chromatographic peak detection using the centWave method
ppm<--method | Integrate areas of missing peaks
ppm<--method | Chromatographic peak detection using the centWave method
ppm<--method | Chromatographic peak detection using the massifquant method
ppm<--method | High resolution peak grouping for single spectra samples
prefilter | Chromatographic peak detection using the centWave method
prefilter-method | Chromatographic peak detection using the centWave method
prefilter-method | Chromatographic peak detection using the massifquant method
prefilter<- | Chromatographic peak detection using the centWave method
prefilter<--method | Chromatographic peak detection using the centWave method
prefilter<--method | Chromatographic peak detection using the massifquant method
present | Determine which peaks are absent / present in a sample class
present-method | Determine which peaks are absent / present in a sample class
processDate | Tracking data processing
processDate-method | Tracking data processing
ProcessHistory | Tracking data processing
processHistory | Data container storing xcms preprocessing results
ProcessHistory-class | Tracking data processing
processHistory-method | Data container storing xcms preprocessing results
processHistoryTypes | Data container storing xcms preprocessing results
processInfo | Tracking data processing
processInfo-method | Tracking data processing
processParam | Tracking data processing
processParam-method | Tracking data processing
processType | Tracking data processing
processType-method | Tracking data processing
profile-matrix | The profile matrix
profinfo | Class xcmsSet, a class for preprocessing peak data
profinfo-method | Class xcmsRaw, a class for handling raw data
profinfo-method | Class xcmsSet, a class for preprocessing peak data
profinfo<- | Class xcmsSet, a class for preprocessing peak data
profinfo<--method | Class xcmsSet, a class for preprocessing peak data
profMat | The profile matrix
profMat-method | Data container storing xcms preprocessing results
profMat-method | The profile matrix
profMat-xcmsSet | The profile matrix
profMedFilt | Median filtering of the profile matrix
profMedFilt-method | Median filtering of the profile matrix
profMethod | Get and set method for generating profile data
profMethod-method | Get and set method for generating profile data
profMethod-method | Class xcmsSet, a class for preprocessing peak data
profMethod<- | Get and set method for generating profile data
profMethod<--method | Get and set method for generating profile data
profMz | Class xcmsRaw, a class for handling raw data
profMz-method | Class xcmsRaw, a class for handling raw data
profRange | Specify a subset of profile mode data
profRange-method | Specify a subset of profile mode data
profStep | Get and set m/z step for generating profile data
profStep-method | Get and set m/z step for generating profile data
profStep-method | Class xcmsSet, a class for preprocessing peak data
profStep<- | Get and set m/z step for generating profile data
profStep<--method | Get and set m/z step for generating profile data
progressCallback | Class xcmsSet, a class for preprocessing peak data
progressCallback-method | Class xcmsSet, a class for preprocessing peak data
progressCallback<- | Class xcmsSet, a class for preprocessing peak data
progressCallback<--method | Class xcmsSet, a class for preprocessing peak data

## -- R --

rawEIC | Get extracted ion chromatograms for specified m/z range
rawEIC-method | Get extracted ion chromatograms for specified m/z range
rawMat | Get a raw data matrix
rawMat-method | Get a raw data matrix
rawMat-methods | Get a raw data matrix
removePeaks-method | XCMSnExp data manipulation methods inherited from MSnbase
response | Align retention times across samples using Obiwarp
response-method | Align retention times across samples using Obiwarp
response<- | Align retention times across samples using Obiwarp
response<--method | Align retention times across samples using Obiwarp
retcor | Correct retention time from different samples
retcor-method | Correct retention time from different samples
retcor-methods | Correct retention time from different samples
retcor.linear | Align retention times across samples
retcor.linear-method | Align retention times across samples
retcor.loess | Align retention times across samples
retcor.loess-method | Align retention times across samples
retcor.obiwarp | Align retention times across samples with Obiwarp
retcor.obiwarp-method | Align retention times across samples with Obiwarp
retcor.peakgroups | Align retention times across samples
retcor.peakgroups-method | Align retention times across samples
retexp | Set retention time window to a specified width
revMz | Class xcmsRaw, a class for handling raw data
revMz-method | Class xcmsRaw, a class for handling raw data
ridgeLength | Single-spectrum non-chromatography MS data peak detection
ridgeLength-method | Single-spectrum non-chromatography MS data peak detection
ridgeLength<- | Single-spectrum non-chromatography MS data peak detection
ridgeLength<--method | Single-spectrum non-chromatography MS data peak detection
roiList | Chromatographic peak detection using the centWave method
roiList-method | Chromatographic peak detection using the centWave method
roiList<- | Chromatographic peak detection using the centWave method
roiList<--method | Chromatographic peak detection using the centWave method
roiScales | Chromatographic peak detection using the centWave method
roiScales-method | Chromatographic peak detection using the centWave method
roiScales<- | Chromatographic peak detection using the centWave method
roiScales<--method | Chromatographic peak detection using the centWave method
rtime-method | Data container storing xcms preprocessing results
rtrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
rtrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms

## -- S --

sampclass | Class xcmsSet, a class for preprocessing peak data
sampclass-method | Class xcmsSet, a class for preprocessing peak data
sampclass<- | Class xcmsSet, a class for preprocessing peak data
sampclass<--method | Class xcmsSet, a class for preprocessing peak data
sampleGroups | Peak grouping based on time dimension peak densities
sampleGroups-method | Peak grouping based on time dimension peak densities
sampleGroups-method | High resolution peak grouping for single spectra samples
sampleGroups-method | Peak grouping based on proximity in the mz-rt space
sampleGroups<- | Peak grouping based on time dimension peak densities
sampleGroups<--method | Peak grouping based on time dimension peak densities
sampleGroups<--method | High resolution peak grouping for single spectra samples
sampleGroups<--method | Peak grouping based on proximity in the mz-rt space
sampnames | Get sample names
sampnames-method | Get sample names
sampnames<- | Class xcmsSet, a class for preprocessing peak data
sampnames<--method | Class xcmsSet, a class for preprocessing peak data
scales | Single-spectrum non-chromatography MS data peak detection
scales-method | Single-spectrum non-chromatography MS data peak detection
scales<- | Single-spectrum non-chromatography MS data peak detection
scales<--method | Single-spectrum non-chromatography MS data peak detection
scanrange | Class xcmsSet, a class for preprocessing peak data
scanrange-method | Class xcmsRaw, a class for handling raw data
scanrange-method | Class xcmsSet, a class for preprocessing peak data
setAs | Data container storing xcms preprocessing results
show-method | Generic parameter class
show-method | Tracking data processing
show-method | Data container storing xcms preprocessing results
show-method | Align retention times across samples using Obiwarp
show-method | Retention time correction based on alignment of house keeping peak groups
show-method | Integrate areas of missing peaks
show-method | Chromatographic peak detection using the centWave method
show-method | Two-step centWave peak detection considering also isotopes
show-method | Chromatographic peak detection using the massifquant method
show-method | Peak detection in the chromatographic time domain
show-method | Single-spectrum non-chromatography MS data peak detection
show-method | Peak grouping based on time dimension peak densities
show-method | High resolution peak grouping for single spectra samples
show-method | Peak grouping based on proximity in the mz-rt space
show-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
show-method | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
show-method | A matrix of peaks
show-method | Class xcmsRaw, a class for handling raw data
show-method | Class xcmsSet, a class for preprocessing peak data
showError | Extract processing errors
showError-method | Extract processing errors
sigma | Peak detection in the chromatographic time domain
sigma-method | Peak detection in the chromatographic time domain
sigma<- | Peak detection in the chromatographic time domain
sigma<--method | Peak detection in the chromatographic time domain
smooth | Retention time correction based on alignment of house keeping peak groups
smooth-method | XCMSnExp data manipulation methods inherited from MSnbase
smooth-method | Retention time correction based on alignment of house keeping peak groups
smooth<- | Retention time correction based on alignment of house keeping peak groups
smooth<--method | Retention time correction based on alignment of house keeping peak groups
snthresh | Chromatographic peak detection using the centWave method
snthresh-method | Chromatographic peak detection using the centWave method
snthresh-method | Chromatographic peak detection using the massifquant method
snthresh-method | Peak detection in the chromatographic time domain
snthresh-method | Single-spectrum non-chromatography MS data peak detection
snthresh<- | Chromatographic peak detection using the centWave method
snthresh<--method | Chromatographic peak detection using the centWave method
snthresh<--method | Chromatographic peak detection using the massifquant method
snthresh<--method | Peak detection in the chromatographic time domain
snthresh<--method | Single-spectrum non-chromatography MS data peak detection
snthreshIsoROIs | Two-step centWave peak detection considering also isotopes
snthreshIsoROIs-method | Two-step centWave peak detection considering also isotopes
snthreshIsoROIs<- | Two-step centWave peak detection considering also isotopes
snthreshIsoROIs<--method | Two-step centWave peak detection considering also isotopes
sortMz | Class xcmsRaw, a class for handling raw data
sortMz-method | Class xcmsRaw, a class for handling raw data
span | Retention time correction based on alignment of house keeping peak groups
span-method | Retention time correction based on alignment of house keeping peak groups
span<- | Retention time correction based on alignment of house keeping peak groups
span<--method | Retention time correction based on alignment of house keeping peak groups
specDist | Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist-method | Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist-methods | Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist.cosine | a Distance function based on matching peaks
specDist.cosine-method | a Distance function based on matching peaks
specDist.meanMZmatch | a Distance function based on matching peaks
specDist.meanMZmatch-method | a Distance function based on matching peaks
specDist.peakCount | a Distance function based on matching peaks
specDist.peakCount-method | a Distance function based on matching peaks
specDist.peakCount-methods | a Distance function based on matching peaks
specNoise | Calculate noise for a sparse continuum mass spectrum
specPeaks | Identify peaks in a sparse continuum mode spectrum
spectra-method | Data container storing xcms preprocessing results
spectrapply-method | Data container storing xcms preprocessing results
split, split-methods | Divide an xcmsSet object
split-method | XCMSnExp filtering and subsetting
split.xcmsRaw | Divide an xcmsRaw object
split.xcmsSet | Divide an xcmsSet object
SSgauss | Gaussian Model
steps | Peak detection in the chromatographic time domain
steps-method | Peak detection in the chromatographic time domain
steps<- | Peak detection in the chromatographic time domain
steps<--method | Peak detection in the chromatographic time domain
stitch | Correct gaps in data
stitch-method | Correct gaps in data
stitch-methods | Correct gaps in data
stitch.netCDF | Correct gaps in data
stitch.xml | Correct gaps in data
subset-xcmsRaw | Subset an xcmsRaw object by scans

## -- T --

tuneIn | Single-spectrum non-chromatography MS data peak detection
tuneIn-method | Single-spectrum non-chromatography MS data peak detection
tuneIn<- | Single-spectrum non-chromatography MS data peak detection
tuneIn<--method | Single-spectrum non-chromatography MS data peak detection

## -- U --

unions | Chromatographic peak detection using the massifquant method
unions-method | Chromatographic peak detection using the massifquant method
unions<- | Chromatographic peak detection using the massifquant method
unions<--method | Chromatographic peak detection using the massifquant method
updateObject-method | Update an 'xcmsSet' object
useOriginalCode | Enable usage of old xcms code

## -- V --

verboseColumns | Chromatographic peak detection using the centWave method
verboseColumns-method | Chromatographic peak detection using the centWave method
verboseColumns-method | Chromatographic peak detection using the massifquant method
verboseColumns-method | Single-spectrum non-chromatography MS data peak detection
verboseColumns<- | Chromatographic peak detection using the centWave method
verboseColumns<--method | Chromatographic peak detection using the centWave method
verboseColumns<--method | Chromatographic peak detection using the massifquant method
verboseColumns<--method | Single-spectrum non-chromatography MS data peak detection
verify.mzQuantML | Verify an mzQuantML file

## -- W --

withWave | Chromatographic peak detection using the massifquant method
withWave-method | Chromatographic peak detection using the massifquant method
withWave<- | Chromatographic peak detection using the massifquant method
withWave<--method | Chromatographic peak detection using the massifquant method
write.cdf | Save an xcmsRaw object to file
write.cdf-method | Save an xcmsRaw object to file
write.mzdata | Save an xcmsRaw object to a file
write.mzdata-method | Save an xcmsRaw object to a file
write.mzQuantML | Save an xcmsSet object to an PSI mzQuantML file
write.mzQuantML-method | Save an xcmsSet object to an PSI mzQuantML file
writeMzTab | Save a grouped xcmsSet object in mzTab-1.1 format file

## -- X --

xcms-deprecated | Deprecated functions in package 'xcms'
xcmsEIC-class | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
xcmsFileSource-class | Base class for loading raw data from a file
xcmsFragments | Constructor for xcmsFragments objects which holds Tandem MS peaks
xcmsFragments-class | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
XCMSnExp | Data container storing xcms preprocessing results
XCMSnExp-class | Data container storing xcms preprocessing results
XCMSnExp-filter | XCMSnExp filtering and subsetting
xcmsPapply | _Deprecated_: xcmsPapply
xcmsPeaks-class | A matrix of peaks
xcmsRaw | Constructor for xcmsRaw objects which reads NetCDF/mzXML files
xcmsRaw-class | Class xcmsRaw, a class for handling raw data
xcmsSet | Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files
xcmsSet-class | Class xcmsSet, a class for preprocessing peak data
xcmsSource | Create an 'xcmsSource' object in a flexible way
xcmsSource-class | Virtual class for raw data sources
xcmsSource-method | Base class for loading raw data from a file
xcmsSource-method | Create an 'xcmsSource' object in a flexible way
xcmsSource-methods | Create an 'xcmsSource' object in a flexible way
XProcessHistory | Tracking data processing
XProcessHistory-class | Tracking data processing

## -- misc --

$-method | Class xcmsSet, a class for preprocessing peak data
$<--method | Class xcmsSet, a class for preprocessing peak data
[-method | XCMSnExp filtering and subsetting
[-method | Subset an xcmsRaw object by scans
[-method | Class xcmsSet, a class for preprocessing peak data
[[-method | XCMSnExp filtering and subsetting