LC-MS and GC-MS Data Analysis

Documentation for package ‘xcms’ version 4.7.2

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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