# LC-MS and GC-MS Data Analysis

## Documentation for package ‘xcms’ version 4.9.0

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

## Help Pages

A B C D E F G H I L M N O P Q 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
adjustedRtime | Data container storing xcms preprocessing results
adjustedRtime-method | Data container storing xcms preprocessing results
adjustedRtime-method | Next Generation 'xcms' Result Object
adjustedRtime<- | Data container storing xcms preprocessing results
adjustedRtime<--method | Data container storing xcms preprocessing results
adjustRtime | Alignment: Retention time correction methods.
adjustRtime-method | Landmark-based alignment: aligning a dataset against an external reference
adjustRtime-method | Alignment: Retention time correction methods.
adjustRtimePeakGroups | Alignment: Retention time correction methods.
adjustRtimePeakGroups-method | xcms result object for very large data sets
applyAdjustedRtime | Replace raw with adjusted retention times
as.list-method | Chromatographic peak detection using the centWave method
as.list-method | Correspondence: group chromatographic peaks across samples
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 --

BetaDistributionParam | Chromatographic peak summaries
bin-method | XCMSnExp data manipulation methods inherited from MSnbase
binSize<--method | Alignment: Retention time correction methods.
binYonX | Aggregate values in y for bins defined on x
BlankFlag | Flag features based on the intensity in blank samples
breaks_on_binSize | Generate breaks for binning using a defined bin size.
breaks_on_nBins | Generate breaks for binning

## -- C --

c, c-methods | Combine xcmsSet objects
c.XcmsExperiment | Next Generation 'xcms' Result Object
c.XCMSnExp | Data container storing xcms preprocessing results
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
centWave | Chromatographic peak detection using the centWave method
CentWaveParam | Chromatographic peak detection using the centWave method
CentWavePredIsoParam | Two-step centWave peak detection considering also isotopes
centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes
chromatogram | Extracting chromatograms
chromatogram-method | Next Generation 'xcms' Result Object
chromatogram-method | Extracting chromatograms
ChromPeakAreaParam | Gap Filling
chromPeakChromatograms | Extract an ion chromatogram for each chromatographic peak
chromPeakChromatograms-method | Extract an ion chromatogram for each chromatographic peak
chromPeakData | Data container storing xcms preprocessing results
chromPeakData-method | Data container storing xcms preprocessing results
chromPeakData-method | Containers for chromatographic and peak detection data
chromPeakData-method | Next Generation 'xcms' Result Object
chromPeakData-method | xcms result object for very large data sets
chromPeakData<- | Data container storing xcms preprocessing results
chromPeakData<--method | Data container storing xcms preprocessing results
chromPeakData<--method | Containers for chromatographic and peak detection data
chromPeakData<--method | Next Generation 'xcms' Result Object
chromPeaks | Data container storing xcms preprocessing results
chromPeaks-method | Data container storing xcms preprocessing results
chromPeaks-method | Containers for chromatographic and peak detection data
chromPeaks-method | Next Generation 'xcms' Result Object
chromPeaks<- | Data container storing xcms preprocessing results
chromPeaks<--method | Data container storing xcms preprocessing results
chromPeaks<--method | Containers for chromatographic and peak detection data
chromPeaks<--method | Next Generation 'xcms' Result Object
chromPeakSpectra | Extract spectra associated with chromatographic peaks
chromPeakSpectra-method | Extract spectra associated with chromatographic peaks
chromPeakSummary | Chromatographic peak summaries
chromPeakSummary-method | Chromatographic peak summaries
clean-method | XCMSnExp data manipulation methods inherited from MSnbase
CleanPeaksParam | Refine Identified Chromatographic Peaks
coerce-method | Containers for chromatographic and peak detection data
collect | Collect MS^n peaks into xcmsFragments
collect-method | Collect MS^n peaks into xcmsFragments
collect-methods | Collect MS^n peaks into xcmsFragments
correlate | Correlate chromatograms
correlate-method | Correlate chromatograms

## -- 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
dirname | Change the file path of an 'OnDiskMSnExp' object
dirname-method | Change the file path of an 'OnDiskMSnExp' object
dirname<--method | Change the file path of an 'OnDiskMSnExp' object
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
DratioFilter | Filter features based on the dispersion ratio
dropAdjustedRtime | Data container storing xcms preprocessing results
dropAdjustedRtime-method | Data container storing xcms preprocessing results
dropAdjustedRtime-method | Next Generation 'xcms' Result Object
dropChromPeaks | Data container storing xcms preprocessing results
dropChromPeaks-method | Data container storing xcms preprocessing results
dropChromPeaks-method | Next Generation 'xcms' Result Object
dropFeatureDefinitions | Data container storing xcms preprocessing results
dropFeatureDefinitions-method | Data container storing xcms preprocessing results
dropFeatureDefinitions-method | Containers for chromatographic and peak detection data
dropFeatureDefinitions-method | Next Generation 'xcms' Result Object
dropFilledChromPeaks | Data container storing xcms preprocessing results
dropFilledChromPeaks-method | Data container storing xcms preprocessing results
dropFilledChromPeaks-method | Containers for chromatographic and peak detection data
dropFilledChromPeaks-method | Next Generation 'xcms' Result Object

## -- E --

EicSimilarityParam | Compounding/feature grouping based on similarity of extracted ion chromatograms
EicSimilarityParam-class | Compounding/feature grouping based on similarity of extracted ion chromatograms
estimatePrecursorIntensity-method | Estimate precursor intensity for MS level 2 spectra
etg | Empirically Transformed Gaussian function
exportMetaboAnalyst | Export data for use in MetaboAnalyst
extractMsData | DEPRECATED: Extract a 'data.frame' containing MS data
extractMsData-method | DEPRECATED: Extract a 'data.frame' containing MS data

## -- F --

faahko_sub | LC-MS preprocessing result test data sets
faahko_sub2 | LC-MS preprocessing result test data sets
feature-grouping | Compounding of LC-MS features
featureArea | Next Generation 'xcms' Result Object
featureArea-method | Next Generation 'xcms' Result Object
featureChromatograms | Extract ion chromatograms for each feature
featureChromatograms-method | Extract ion chromatograms for each feature
featureDefinitions | Data container storing xcms preprocessing results
featureDefinitions-method | Data container storing xcms preprocessing results
featureDefinitions-method | Containers for chromatographic and peak detection data
featureDefinitions-method | Next Generation 'xcms' Result Object
featureDefinitions<- | Data container storing xcms preprocessing results
featureDefinitions<--method | Data container storing xcms preprocessing results
featureDefinitions<--method | Next Generation 'xcms' Result Object
featureGroups-method | Compounding of LC-MS features
featureGroups<--method | Compounding of LC-MS features
featureSpectra | Extract spectra associated with features
featureSpectra-method | Extract spectra associated with features
featureSummary | Simple feature summaries
featureValues | Accessing mz-rt feature data values
featureValues-method | Accessing mz-rt feature data values
featureValues-method | Containers for chromatographic and peak detection data
featureValues-method | Next Generation 'xcms' Result Object
fileIndex | Tracking data processing
fileIndex-method | Tracking data processing
fileNames-method | Next Generation 'xcms' Result Object
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 | Gap Filling
fillChromPeaks-method | Gap Filling
FillChromPeaksParam | Gap Filling
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
filterChromPeaks | Next Generation 'xcms' Result Object
filterChromPeaks-method | XCMSnExp filtering and subsetting
filterChromPeaks-method | Containers for chromatographic and peak detection data
filterChromPeaks-method | Next Generation 'xcms' Result Object
filterChromPeaks-method | xcms result object for very large data sets
filterColumnsIntensityAbove | Filtering sets of chromatographic data
filterColumnsIntensityAbove-method | Filtering sets of chromatographic data
filterColumnsKeepTop | Filtering sets of chromatographic data
filterColumnsKeepTop-method | Filtering sets of chromatographic data
filterFeatureDefinitions | Next Generation 'xcms' Result Object
filterFeatureDefinitions-method | XCMSnExp filtering and subsetting
filterFeatureDefinitions-method | Next Generation 'xcms' Result Object
filterFeatureDefinitions-method | xcms result object for very large data sets
filterFeatures | Filtering of features based on conventional quality assessment
filterFeatures-method | Flag features based on the intensity in blank samples
filterFeatures-method | Filter features based on the dispersion ratio
filterFeatures-method | Filter features based on the percentage of missing data
filterFeatures-method | Filter features based on their coefficient of variation
filterFile-method | XCMSnExp filtering and subsetting
filterFile-method | Next Generation 'xcms' Result Object
FilterIntensityParam | Refine Identified Chromatographic Peaks
filterIsolationWindow-method | Next Generation 'xcms' Result Object
filterMsLevel-method | XCMSnExp filtering and subsetting
filterMsLevel-method | Next Generation 'xcms' Result Object
filterMz-method | XCMSnExp filtering and subsetting
filterMz-method | Containers for chromatographic and peak detection data
filterMz-method | Next Generation 'xcms' Result Object
filterMzRange-method | Next Generation 'xcms' Result Object
filterRt-method | XCMSnExp filtering and subsetting
filterRt-method | Containers for chromatographic and peak detection data
filterRt-method | Next Generation 'xcms' Result Object
findChromPeaks | Chromatographic Peak Detection
findChromPeaks-centWave | Chromatographic peak detection using the centWave method
findChromPeaks-centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes
findChromPeaks-Chromatogram-CentWaveParam | centWave-based peak detection in purely chromatographic data
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 | centWave-based peak detection in purely chromatographic data
findChromPeaks-method | matchedFilter-based peak detection in purely chromatographic data
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 | Chromatographic Peak Detection
findChromPeaks-method | Single-spectrum non-chromatography MS data peak detection
findChromPeaksIsolationWindow | Data independent acquisition (DIA): peak detection in isolation windows
findChromPeaksIsolationWindow-method | Data independent acquisition (DIA): peak detection in isolation windows
findMZ | Find fragment ions in xcmsFragment objects
findMZ-method | Find fragment ions in xcmsFragment objects
findmzROI | Class xcmsRaw, a class for handling raw data
findmzROI-method | Class xcmsRaw, a class for handling raw data
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
fromFile-method | Next Generation 'xcms' Result Object

## -- G --

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: group chromatographic peaks across samples
groupChromPeaks-method | Containers for chromatographic and peak detection data
groupChromPeaks-method | Correspondence: group chromatographic peaks across samples
groupFeatures-abundance-correlation | Compounding/feature grouping based on similarity of abundances across samples
groupFeatures-eic-similarity | Compounding/feature grouping based on similarity of extracted ion chromatograms
groupFeatures-method | Compounding/feature grouping based on similarity of abundances across samples
groupFeatures-method | Compounding/feature grouping based on similarity of extracted ion chromatograms
groupFeatures-method | Compounding/feature grouping based on similar retention times
groupFeatures-similar-rtime | Compounding/feature grouping based on similar retention times
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 unique group (feature) names based on mass and retention time
groupnames-method | Generate unque names for peak groups
groupOverlaps | Group overlapping ranges
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
hasAdjustedRtime-method | Next Generation 'xcms' Result Object
hasChromPeaks | Data container storing xcms preprocessing results
hasChromPeaks-method | Data container storing xcms preprocessing results
hasChromPeaks-method | Containers for chromatographic and peak detection data
hasChromPeaks-method | Next Generation 'xcms' Result Object
hasFeatures | Data container storing xcms preprocessing results
hasFeatures-method | Data container storing xcms preprocessing results
hasFeatures-method | Containers for chromatographic and peak detection data
hasFeatures-method | Next Generation 'xcms' Result Object
hasFilledChromPeaks | Data container storing xcms preprocessing results
hasFilledChromPeaks-method | Data container storing xcms preprocessing results
hasFilledChromPeaks-method | Containers for chromatographic and peak detection data
hasFilledChromPeaks-method | Next Generation 'xcms' Result Object
highlightChromPeaks | Add definition of chromatographic peaks to an extracted chromatogram plot

## -- I --

image-method | Plot log intensity image of a xcmsRaw object
imputeLinInterpol | Impute values for empty elements in a vector using linear interpolation
imputeRowMin | Replace missing values with a proportion of the row minimum
imputeRowMinRand | Impute missing values with random numbers based on the row minimum
intensity-method | Data container storing xcms preprocessing results
isCalibrated | Calibrant mass based calibration of chromatgraphic peaks
isolationWindowTargetMz | Extract isolation window target m/z definition
isolationWindowTargetMz-method | Extract isolation window target m/z definition

## -- L --

LamaParama | Landmark-based alignment: aligning a dataset against an external reference
LamaParama-class | Landmark-based alignment: aligning a dataset against an external reference
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
loadXcmsData | LC-MS preprocessing result test data sets

## -- M --

makeacqNum | Correct gaps in data
makeacqNum-method | Correct gaps in data
manualChromPeaks | Manual peak integration and feature definition
manualChromPeaks-method | Manual peak integration and feature definition
manualFeatures | Manual peak integration and feature definition
manualFeatures-method | Manual peak integration and feature definition
massifquant | Chromatographic peak detection using the massifquant method
MassifquantParam | Chromatographic peak detection using the massifquant method
matchedFilter | Peak detection in the chromatographic time domain
MatchedFilterParam | Peak detection in the chromatographic time domain
matchedRtimes | Landmark-based alignment: aligning a dataset against an external reference
matchLamasChromPeaks | Landmark-based alignment: aligning a dataset against an external reference
medianFilter | Apply a median filter to a matrix
MergeNeighboringPeaksParam | Refine Identified Chromatographic Peaks
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
mz,CalibrantMassParam | Calibrant mass based calibration of chromatgraphic peaks
mz-method | Data container storing xcms preprocessing results
MzClustParam | Correspondence: group chromatographic peaks across samples
mzrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
mzrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms

## -- N --

NearestPeaksParam | Correspondence: group chromatographic peaks across samples
normalize-method | XCMSnExp data manipulation methods inherited from MSnbase

## -- O --

ObiwarpParam | Alignment: Retention time correction methods.
overlappingFeatures | Identify overlapping features

## -- P --

Param | Generic parameter class
PeakDensityParam | Correspondence: group chromatographic peaks across samples
PeakGroupsParam | Alignment: Retention time correction methods.
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
peaksWithCentWave | Identify peaks in chromatographic data using centWave
peaksWithMatchedFilter | Identify peaks in chromatographic data using matchedFilter
peakTable | Create report of aligned peak intensities
peakTable-method | Create report of aligned peak intensities
PercentMissingFilter | Filter features based on the percentage of missing data
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-method | Landmark-based alignment: aligning a dataset against an external reference
plot-method | Data container storing xcms preprocessing results
plot-method | Containers for chromatographic and peak detection data
plot-method | Next Generation 'xcms' Result Object
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
plotChromatogramsOverlay | Plot multiple chromatograms into the same plot
plotChromatogramsOverlay-method | Plot multiple chromatograms into the same plot
plotChromPeakDensity | Plot chromatographic peak density along the retention time axis
plotChromPeakDensity-method | Containers for chromatographic and peak detection data
plotChromPeakDensity-method | 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
plotFeatureGroups | Plot feature groups in the m/z-retention time space
plotMsData | DEPRECATED: 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
plotPrecursorIons | General visualization of precursor ions of LC-MS/MS data
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 | Next Generation 'xcms' Result Object
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
processHistory-method | Containers for chromatographic and peak detection data
processHistory-method | Next Generation 'xcms' Result Object
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

## -- Q --

quantify | Next Generation 'xcms' Result Object
quantify-method | Accessing mz-rt feature data values
quantify-method | Next Generation 'xcms' Result Object

## -- 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
reconstructChromPeakSpectra | Data independent acquisition (DIA): reconstruct MS2 spectra
reconstructChromPeakSpectra-method | Data independent acquisition (DIA): reconstruct MS2 spectra
refineChromPeaks | Refine Identified Chromatographic Peaks
refineChromPeaks-method | Containers for chromatographic and peak detection data
refineChromPeaks-method | Refine Identified Chromatographic Peaks
removeIntensity | Remove intensities from chromatographic data
removeIntensity-method | Remove intensities from chromatographic data
removePeaks-method | XCMSnExp data manipulation methods inherited from MSnbase
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
rla | Calculate relative log abundances
rowRla | Calculate relative log abundances
RsdFilter | Filter features based on their coefficient of variation
rtime-method | Data container storing xcms preprocessing results
rtime-method | Next Generation 'xcms' Result Object
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
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
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
showError | Extract processing errors
showError-method | Extract processing errors
smooth-method | XCMSnExp data manipulation methods inherited from MSnbase
sortMz | Class xcmsRaw, a class for handling raw data
sortMz-method | Class xcmsRaw, a class for handling raw data
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
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
summarizeLamaMatch | Landmark-based alignment: aligning a dataset against an external reference

## -- T --

toXcmsExperiment | xcms result object for very large data sets
toXcmsExperimentHdf5 | xcms result object for very large data sets
transformIntensity-method | Containers for chromatographic and peak detection data

## -- U --

uniqueMsLevels-method | Next Generation 'xcms' Result Object
updateObject-method | Data container storing xcms preprocessing results
updateObject-method | Update an 'xcmsSet' object
useOriginalCode | Enable usage of old xcms code

## -- V --

verify.mzQuantML | Verify an mzQuantML file

## -- W --

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
writeMSData-method | Export MS data to mzML/mzXML files
writeMzTab | Save a grouped xcmsSet object in mzTab-1.1 format file

## -- X --

XChromatogram | Containers for chromatographic and peak detection data
XChromatogram-class | Containers for chromatographic and peak detection data
XChromatograms | Containers for chromatographic and peak detection data
XChromatograms-class | Containers for chromatographic and peak detection data
xcms-deprecated | Deprecated functions in package 'xcms'
xcmsEIC-class | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
XcmsExperiment | Next Generation 'xcms' Result Object
XcmsExperiment-class | Next Generation 'xcms' Result Object
XcmsExperimentHdf5 | xcms result object for very large data sets
XcmsExperimentHdf5-class | xcms result object for very large data sets
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
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
xdata | LC-MS preprocessing result test data sets
xmse | LC-MS preprocessing result test data sets
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 | Containers for chromatographic and peak detection data
[-method | Next Generation 'xcms' Result Object
[-method | Subset an xcmsRaw object by scans
[-method | Class xcmsSet, a class for preprocessing peak data
[[-method | XCMSnExp filtering and subsetting