A B C D E F G H I L M N O P Q R S T U V W X misc
| 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' ~~ | 
| 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-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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| NearestPeaksParam | Correspondence: group chromatographic peaks across samples | 
| normalize-method | XCMSnExp data manipulation methods inherited from MSnbase | 
| ObiwarpParam | Alignment: Retention time correction methods. | 
| overlappingFeatures | Identify overlapping features | 
| 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 | 
| quantify | Next Generation 'xcms' Result Object | 
| quantify-method | Accessing mz-rt feature data values | 
| quantify-method | Next Generation 'xcms' Result Object | 
| 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 | 
| 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 | 
| 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 | 
| 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 | 
| verify.mzQuantML | Verify an mzQuantML file | 
| 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 | 
| 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 | 
| $-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 |