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A B C D E F G H I K 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 |
| absMz | High resolution peak grouping for single spectra samples |
| absMz-method | High resolution peak grouping for single spectra samples |
| absMz-method | Peak grouping based on proximity in the mz-rt space |
| absMz<- | High resolution peak grouping for single spectra samples |
| absMz<--method | High resolution peak grouping for single spectra samples |
| absMz<--method | Peak grouping based on proximity in the mz-rt space |
| absRt | Peak grouping based on proximity in the mz-rt space |
| absRt-method | Peak grouping based on proximity in the mz-rt space |
| absRt<- | Peak grouping based on proximity in the mz-rt space |
| absRt<--method | Peak grouping based on proximity in the mz-rt space |
| addParams | Single-spectrum non-chromatography MS data peak detection |
| addParams-method | Single-spectrum non-chromatography MS data peak detection |
| addParams<- | Single-spectrum non-chromatography MS data peak detection |
| addParams<--method | Single-spectrum non-chromatography MS data peak detection |
| adjustedRtime | Data container storing xcms preprocessing results |
| adjustedRtime-method | Data container storing xcms preprocessing results |
| adjustedRtime<- | Data container storing xcms preprocessing results |
| adjustedRtime<--method | Data container storing xcms preprocessing results |
| adjustRtime | Alignment: Retention time correction methods. |
| adjustRtime-method | Align retention times across samples using Obiwarp |
| adjustRtime-method | Retention time correction based on alignment of house keeping peak groups |
| adjustRtime-obiwarp | Align retention times across samples using Obiwarp |
| adjustRtime-peakGroups | Retention time correction based on alignment of house keeping peak groups |
| adjustRtimePeakGroups | Retention time correction based on alignment of house keeping peak groups |
| align | Aligning chromatographic data |
| align-method | Aligning chromatographic data |
| ampTh | Single-spectrum non-chromatography MS data peak detection |
| ampTh-method | Single-spectrum non-chromatography MS data peak detection |
| ampTh<- | Single-spectrum non-chromatography MS data peak detection |
| ampTh<--method | Single-spectrum non-chromatography MS data peak detection |
| applyAdjustedRtime | Replace raw with adjusted retention times |
| AutoLockMass | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
| AutoLockMass-method | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
| AutoLockMass-methods | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
| baseValue | Peak detection in the chromatographic time domain |
| baseValue-method | Peak detection in the chromatographic time domain |
| baseValue<- | Peak detection in the chromatographic time domain |
| baseValue<--method | Peak detection in the chromatographic time domain |
| bin-method | XCMSnExp data manipulation methods inherited from MSnbase |
| binSize | Peak detection in the chromatographic time domain |
| binSize-method | Align retention times across samples using Obiwarp |
| binSize-method | Peak detection in the chromatographic time domain |
| binSize-method | Peak grouping based on time dimension peak densities |
| binSize<- | Peak detection in the chromatographic time domain |
| binSize<--method | Align retention times across samples using Obiwarp |
| binSize<--method | Peak detection in the chromatographic time domain |
| binSize<--method | Peak grouping based on time dimension peak densities |
| binYonX | Aggregate values in y for bins defined on x |
| breaks_on_binSize | Generate breaks for binning using a defined bin size. |
| breaks_on_nBins | Generate breaks for binning |
| bw | Peak grouping based on time dimension peak densities |
| bw-method | Peak grouping based on time dimension peak densities |
| bw<- | Peak grouping based on time dimension peak densities |
| bw<--method | Peak grouping based on time dimension peak densities |
| c, c-methods | Combine xcmsSet objects |
| 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 |
| centerSample | Align retention times across samples using Obiwarp |
| centerSample-method | Align retention times across samples using Obiwarp |
| centerSample<- | Align retention times across samples using Obiwarp |
| centerSample<--method | Align retention times across samples using Obiwarp |
| centWave | Chromatographic peak detection using the centWave method |
| CentWaveParam | Chromatographic peak detection using the centWave method |
| CentWaveParam-class | Chromatographic peak detection using the centWave method |
| CentWavePredIsoParam | Two-step centWave peak detection considering also isotopes |
| CentWavePredIsoParam-class | Two-step centWave peak detection considering also isotopes |
| centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes |
| checkBack | Chromatographic peak detection using the massifquant method |
| checkBack-method | Chromatographic peak detection using the massifquant method |
| checkBack<- | Chromatographic peak detection using the massifquant method |
| checkBack<--method | Chromatographic peak detection using the massifquant method |
| chromatogram | Extracting chromatograms |
| chromatogram-method | Extracting chromatograms |
| chromatographic-peak-detection | Chromatographic peak detection methods. |
| ChromPeakAreaParam | Integrate areas of missing peaks |
| ChromPeakAreaParam-class | Integrate areas of missing peaks |
| 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<- | Data container storing xcms preprocessing results |
| chromPeakData<--method | Data container storing xcms preprocessing results |
| chromPeakData<--method | Containers for chromatographic and peak detection data |
| 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<- | Data container storing xcms preprocessing results |
| chromPeaks<--method | Data container storing xcms preprocessing results |
| chromPeaks<--method | Containers for chromatographic and peak detection data |
| chromPeakSpectra | Extract (MS2) spectra associated with chromatographic peaks |
| class:Param | Generic parameter class |
| clean-method | XCMSnExp data manipulation methods inherited from MSnbase |
| CleanPeaksParam | Remove chromatographic peaks with too large rt width |
| CleanPeaksParam-class | Remove chromatographic peaks with too large rt width |
| 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 |
| consecMissedLimit | Chromatographic peak detection using the massifquant method |
| consecMissedLimit-method | Chromatographic peak detection using the massifquant method |
| consecMissedLimit<- | Chromatographic peak detection using the massifquant method |
| consecMissedLimit<--method | Chromatographic peak detection using the massifquant method |
| correlate | Correlate chromatograms |
| correlate-method | Correlate chromatograms |
| criticalValue | Chromatographic peak detection using the massifquant method |
| criticalValue-method | Chromatographic peak detection using the massifquant method |
| criticalValue<- | Chromatographic peak detection using the massifquant method |
| criticalValue<--method | Chromatographic peak detection using the massifquant method |
| 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 |
| distance | Peak detection in the chromatographic time domain |
| distance-method | Peak detection in the chromatographic time domain |
| distance<- | Peak detection in the chromatographic time domain |
| distance<--method | Peak detection in the chromatographic time domain |
| distFun | Align retention times across samples using Obiwarp |
| distFun-method | Align retention times across samples using Obiwarp |
| distFun<- | Align retention times across samples using Obiwarp |
| distFun<--method | Align retention times across samples using Obiwarp |
| do_adjustRtime_peakGroups | Align spectrum retention times across samples using peak groups found in most samples |
| do_findChromPeaks_addPredIsoROIs | Core API function for two-step centWave peak detection with isotopes |
| do_findChromPeaks_centWave | Core API function for centWave peak detection |
| do_findChromPeaks_centWaveWithPredIsoROIs | Core API function for two-step centWave peak detection with isotopes |
| do_findChromPeaks_massifquant | Core API function for massifquant peak detection |
| do_findChromPeaks_matchedFilter | Core API function for matchedFilter peak detection |
| do_findPeaks_MSW | Core API function for single-spectrum non-chromatography MS data peak detection |
| do_groupChromPeaks_density | Core API function for peak density based chromatographic peak grouping |
| do_groupChromPeaks_nearest | Core API function for chromatic peak grouping using a nearest neighbor approach |
| do_groupPeaks_mzClust | Core API function for peak grouping using mzClust |
| dropAdjustedRtime | Data container storing xcms preprocessing results |
| dropAdjustedRtime-method | Data container storing xcms preprocessing results |
| dropChromPeaks | Data container storing xcms preprocessing results |
| dropChromPeaks-method | Data container storing xcms preprocessing results |
| dropFeatureDefinitions | Data container storing xcms preprocessing results |
| dropFeatureDefinitions-method | Data container storing xcms preprocessing results |
| dropFeatureDefinitions-method | Containers for chromatographic and peak detection data |
| dropFilledChromPeaks | Data container storing xcms preprocessing results |
| dropFilledChromPeaks-method | Data container storing xcms preprocessing results |
| dropFilledChromPeaks-method | Containers for chromatographic and peak detection data |
| estimatePrecursorIntensity | Estimate precursor intensity for MS level 2 spectra |
| etg | Empirically Transformed Gaussian function |
| expandMz | Integrate areas of missing peaks |
| expandMz-method | Integrate areas of missing peaks |
| expandMz<- | Integrate areas of missing peaks |
| expandMz<--method | Integrate areas of missing peaks |
| expandRt | Integrate areas of missing peaks |
| expandRt-method | Integrate areas of missing peaks |
| expandRt<- | Integrate areas of missing peaks |
| expandRt<--method | Integrate areas of missing peaks |
| 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 |
| extraPeaks | Retention time correction based on alignment of house keeping peak groups |
| extraPeaks-method | Retention time correction based on alignment of house keeping peak groups |
| extraPeaks<- | Retention time correction based on alignment of house keeping peak groups |
| extraPeaks<--method | Retention time correction based on alignment of house keeping peak groups |
| faahko_sub | Data container storing xcms preprocessing results |
| factorDiag | Align retention times across samples using Obiwarp |
| factorDiag-method | Align retention times across samples using Obiwarp |
| factorDiag<- | Align retention times across samples using Obiwarp |
| factorDiag<--method | Align retention times across samples using Obiwarp |
| factorGap | Align retention times across samples using Obiwarp |
| factorGap-method | Align retention times across samples using Obiwarp |
| factorGap<- | Align retention times across samples using Obiwarp |
| factorGap<--method | Align retention times across samples using Obiwarp |
| family | Retention time correction based on alignment of house keeping peak groups |
| family-method | Retention time correction based on alignment of house keeping peak groups |
| family<- | Retention time correction based on alignment of house keeping peak groups |
| family<--method | Retention time correction based on alignment of house keeping peak groups |
| featureChromatograms | 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<- | Data container storing xcms preprocessing results |
| featureDefinitions<--method | Data container storing xcms preprocessing results |
| featureSpectra | Extract (MS2) 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 |
| fileIndex | Tracking data processing |
| fileIndex-method | Tracking data processing |
| filepaths | Class xcmsSet, a class for preprocessing peak data |
| filepaths-method | Class xcmsSet, a class for preprocessing peak data |
| filepaths<- | Class xcmsSet, a class for preprocessing peak data |
| filepaths<--method | Class xcmsSet, a class for preprocessing peak data |
| fillChromPeaks | Integrate areas of missing peaks |
| fillChromPeaks-method | Integrate areas of missing peaks |
| FillChromPeaksParam | Integrate areas of missing peaks |
| FillChromPeaksParam-class | Integrate areas of missing peaks |
| fillPeaks | Integrate areas of missing peaks |
| fillPeaks-method | Integrate areas of missing peaks |
| fillPeaks.chrom | Integrate areas of missing peaks |
| fillPeaks.chrom-method | Integrate areas of missing peaks |
| fillPeaks.MSW | Integrate areas of missing peaks in FTICR-MS data |
| fillPeaks.MSW-method | Integrate areas of missing peaks in FTICR-MS data |
| filterAcquisitionNum-method | XCMSnExp data manipulation methods inherited from MSnbase |
| 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 | XCMSnExp filtering and subsetting |
| filterFile-method | XCMSnExp filtering and subsetting |
| FilterIntensityParam | Remove chromatographic peaks based on intensity |
| FilterIntensityParam-class | Remove chromatographic peaks based on intensity |
| filterMsLevel-method | XCMSnExp filtering and subsetting |
| filterMz-method | XCMSnExp filtering and subsetting |
| filterMz-method | Containers for chromatographic and peak detection data |
| filterRt-method | XCMSnExp filtering and subsetting |
| filterRt-method | Containers for chromatographic and peak detection data |
| findChromPeaks | Chromatographic peak detection methods. |
| findChromPeaks-centWave | Chromatographic peak detection using the centWave method |
| findChromPeaks-centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes |
| findChromPeaks-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 | Single-spectrum non-chromatography MS data peak detection |
| findChromPeaksIsolationWindow | Data independent acquisition (DIA): peak detection in isolation windows |
| findMZ | Find fragment ions in xcmsFragment objects |
| findMZ-method | Find fragment ions in xcmsFragment objects |
| findneutral | Find neutral losses in xcmsFragment objects |
| findneutral-method | Find neutral losses in xcmsFragment objects |
| findPeaks | Feature detection for GC/MS and LC/MS Data - methods |
| findPeaks-method | Feature detection for GC/MS and LC/MS Data - methods |
| findPeaks-methods | Feature detection for GC/MS and LC/MS Data - methods |
| findPeaks-MSW | Single-spectrum non-chromatography MS data peak detection |
| findPeaks.addPredictedIsotopeFeatures | Feature detection based on predicted isotope features for high resolution LC/MS data |
| findPeaks.addPredictedIsotopeFeatures-method | Feature detection based on predicted isotope features for high resolution LC/MS data |
| findPeaks.centWave | Feature detection for high resolution LC/MS data |
| findPeaks.centWave-method | Feature detection for high resolution LC/MS data |
| findPeaks.centWaveWithPredictedIsotopeROIs | Feature detection with centWave and additional isotope features |
| findPeaks.centWaveWithPredictedIsotopeROIs-method | Feature detection with centWave and additional isotope features |
| findPeaks.massifquant | Feature detection for XC-MS data. |
| findPeaks.massifquant-method | Feature detection for XC-MS data. |
| findPeaks.matchedFilter | Peak detection in the chromatographic time domain |
| findPeaks.matchedFilter-method | Peak detection in the chromatographic time domain |
| findPeaks.MS1 | Collecting MS1 precursor peaks |
| findPeaks.MS1-method | Collecting MS1 precursor peaks |
| findPeaks.MSW | Peak detection for single-spectrum non-chromatography MS data |
| findPeaks.MSW-method | Peak detection for single-spectrum non-chromatography MS data |
| firstBaselineCheck | Chromatographic peak detection using the centWave method |
| firstBaselineCheck-method | Chromatographic peak detection using the centWave method |
| firstBaselineCheck<- | Chromatographic peak detection using the centWave method |
| firstBaselineCheck<--method | Chromatographic peak detection using the centWave method |
| fitgauss | Chromatographic peak detection using the centWave method |
| fitgauss-method | Chromatographic peak detection using the centWave method |
| fitgauss-method | Chromatographic peak detection using the massifquant method |
| fitgauss<- | Chromatographic peak detection using the centWave method |
| fitgauss<--method | Chromatographic peak detection using the centWave method |
| fitgauss<--method | Chromatographic peak detection using the massifquant method |
| fixedMz | Integrate areas of missing peaks |
| fixedRt | Integrate areas of missing peaks |
| fwhm | Peak detection in the chromatographic time domain |
| fwhm-method | Peak detection in the chromatographic time domain |
| fwhm<- | Peak detection in the chromatographic time domain |
| fwhm<--method | Peak detection in the chromatographic time domain |
| gapExtend | Align retention times across samples using Obiwarp |
| gapExtend-method | Align retention times across samples using Obiwarp |
| gapExtend<- | Align retention times across samples using Obiwarp |
| gapExtend<--method | Align retention times across samples using Obiwarp |
| gapInit | Align retention times across samples using Obiwarp |
| gapInit-method | Align retention times across samples using Obiwarp |
| gapInit<- | Align retention times across samples using Obiwarp |
| gapInit<--method | Align retention times across samples using Obiwarp |
| GenericParam | Generic parameter class |
| GenericParam-class | Generic parameter class |
| getEIC | Get extracted ion chromatograms for specified m/z ranges |
| getEIC-method | Get extracted ion chromatograms for specified m/z ranges |
| getMsnScan | Get m/z and intensity values for a single mass scan |
| getMsnScan-method | Get m/z and intensity values for a single mass scan |
| getPeaks | Get peak intensities for specified regions |
| getPeaks-method | Get peak intensities for specified regions |
| getScan | Get m/z and intensity values for a single mass scan |
| getScan-method | Get m/z and intensity values for a single mass scan |
| getSpec | Get average m/z and intensity values for multiple mass scans |
| getSpec-method | Get average m/z and intensity values for multiple mass scans |
| getXcmsRaw | Load the raw data for one or more files in the xcmsSet |
| getXcmsRaw-method | Load the raw data for one or more files in the xcmsSet |
| group | Group peaks from different samples together |
| group-method | Group peaks from different samples together |
| group-methods | Group peaks from different samples together |
| group.density | Group peaks from different samples together |
| group.density-method | Group peaks from different samples together |
| group.mzClust | Group Peaks via High Resolution Alignment |
| group.mzClust-method | Group Peaks via High Resolution Alignment |
| group.nearest | Group peaks from different samples together |
| group.nearest-method | Group peaks from different samples together |
| groupChromPeaks | Correspondence: Chromatographic peak grouping methods. |
| groupChromPeaks-density | Peak grouping based on time dimension peak densities |
| groupChromPeaks-method | Containers for chromatographic and peak detection data |
| groupChromPeaks-method | Peak grouping based on time dimension peak densities |
| groupChromPeaks-method | High resolution peak grouping for single spectra samples |
| groupChromPeaks-method | Peak grouping based on proximity in the mz-rt space |
| groupChromPeaks-mzClust | High resolution peak grouping for single spectra samples |
| groupChromPeaks-nearest | Peak grouping based on proximity in the mz-rt space |
| groupidx | Class xcmsSet, a class for preprocessing peak data |
| groupidx-method | Class xcmsSet, a class for preprocessing peak data |
| groupidx<- | Class xcmsSet, a class for preprocessing peak data |
| groupidx<--method | Class xcmsSet, a class for preprocessing peak data |
| groupnames | Generate unque names for peak groups |
| groupnames-method | Generate 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 |
| hasChromPeaks | Data container storing xcms preprocessing results |
| hasChromPeaks-method | Data container storing xcms preprocessing results |
| hasChromPeaks-method | Containers for chromatographic and peak detection data |
| hasFeatures | Data container storing xcms preprocessing results |
| hasFeatures-method | Data container storing xcms preprocessing results |
| hasFeatures-method | Containers for chromatographic and peak detection data |
| hasFilledChromPeaks | Data container storing xcms preprocessing results |
| hasFilledChromPeaks-method | Data container storing xcms preprocessing results |
| hasFilledChromPeaks-method | Containers for chromatographic and peak detection data |
| highlightChromPeaks | Add definition of chromatographic peaks to an extracted chromatogram plot |
| image-method | Plot log intensity image of a xcmsRaw object |
| impute-method | Peak detection in the chromatographic time domain |
| impute<- | Peak detection in the chromatographic time domain |
| impute<--method | Peak detection in the chromatographic time domain |
| imputeLinInterpol | Impute values for empty elements in a vector using linear interpolation |
| imputeRowMin | Replace missing values with a proportion of the row minimum |
| imputeRowMinRand | Impute missing values with random numbers based on the row minimum |
| index | Peak detection in the chromatographic time domain |
| index-method | Peak detection in the chromatographic time domain |
| index<- | Peak detection in the chromatographic time domain |
| index<--method | Peak detection in the chromatographic time domain |
| initPenalty | Align retention times across samples using Obiwarp |
| initPenalty-method | Align retention times across samples using Obiwarp |
| initPenalty<- | Align retention times across samples using Obiwarp |
| initPenalty<--method | Align retention times across samples using Obiwarp |
| integrate-method | Chromatographic peak detection using the centWave method |
| integrate-method | Chromatographic peak detection using the massifquant method |
| integrate<- | Chromatographic peak detection using the centWave method |
| integrate<--method | Chromatographic peak detection using the centWave method |
| integrate<--method | Chromatographic peak detection using the massifquant method |
| intensity-method | Data container storing xcms preprocessing results |
| isCalibrated | Calibrant mass based calibration of chromatgraphic peaks |
| isolationWindowTargetMz | Extract isolation window target m/z definition |
| isolationWindowTargetMz-method | Extract isolation window target m/z definition |
| kNN | Peak grouping based on proximity in the mz-rt space |
| kNN-method | Peak grouping based on proximity in the mz-rt space |
| kNN<- | Peak grouping based on proximity in the mz-rt space |
| kNN<--method | Peak grouping based on proximity in the mz-rt space |
| levelplot | Class xcmsRaw, a class for handling raw data |
| levelplot-method | Plot log intensity image of a xcmsRaw object |
| loadRaw | Read binary data from a source |
| loadRaw-method | Read binary data from a source |
| loadRaw-methods | Read binary data from a source |
| localAlignment | Align retention times across samples using Obiwarp |
| localAlignment-method | Align retention times across samples using Obiwarp |
| localAlignment<- | Align retention times across samples using Obiwarp |
| localAlignment<--method | Align retention times across samples using Obiwarp |
| makeacqNum | Correct gaps in data |
| makeacqNum-method | Correct gaps in data |
| massifquant | Chromatographic peak detection using the massifquant method |
| MassifquantParam | Chromatographic peak detection using the massifquant method |
| MassifquantParam-class | Chromatographic peak detection using the massifquant method |
| matchedFilter | Peak detection in the chromatographic time domain |
| MatchedFilterParam | Peak detection in the chromatographic time domain |
| MatchedFilterParam-class | Peak detection in the chromatographic time domain |
| max-method | Peak detection in the chromatographic time domain |
| max<- | Peak detection in the chromatographic time domain |
| max<--method | Peak detection in the chromatographic time domain |
| maxCharge | Two-step centWave peak detection considering also isotopes |
| maxCharge-method | Two-step centWave peak detection considering also isotopes |
| maxCharge<- | Two-step centWave peak detection considering also isotopes |
| maxCharge<--method | Two-step centWave peak detection considering also isotopes |
| maxFeatures | Peak grouping based on time dimension peak densities |
| maxFeatures-method | Peak grouping based on time dimension peak densities |
| maxFeatures<- | Peak grouping based on time dimension peak densities |
| maxFeatures<--method | Peak grouping based on time dimension peak densities |
| maxIso | Two-step centWave peak detection considering also isotopes |
| maxIso-method | Two-step centWave peak detection considering also isotopes |
| maxIso<- | Two-step centWave peak detection considering also isotopes |
| maxIso<--method | Two-step centWave peak detection considering also isotopes |
| medianFilter | Apply a median filter to a matrix |
| MergeNeighboringPeaksParam | Merge neighboring and overlapping chromatographic peaks |
| MergeNeighboringPeaksParam-class | Merge neighboring and overlapping chromatographic peaks |
| minFraction | Peak grouping based on time dimension peak densities |
| minFraction-method | Retention time correction based on alignment of house keeping peak groups |
| minFraction-method | Peak grouping based on time dimension peak densities |
| minFraction-method | High resolution peak grouping for single spectra samples |
| minFraction<- | Peak grouping based on time dimension peak densities |
| minFraction<--method | Retention time correction based on alignment of house keeping peak groups |
| minFraction<--method | Peak grouping based on time dimension peak densities |
| minFraction<--method | High resolution peak grouping for single spectra samples |
| minNoiseLevel | Single-spectrum non-chromatography MS data peak detection |
| minNoiseLevel-method | Single-spectrum non-chromatography MS data peak detection |
| minNoiseLevel<- | Single-spectrum non-chromatography MS data peak detection |
| minNoiseLevel<--method | Single-spectrum non-chromatography MS data peak detection |
| minSamples | Peak grouping based on time dimension peak densities |
| minSamples-method | Peak grouping based on time dimension peak densities |
| minSamples-method | High resolution peak grouping for single spectra samples |
| minSamples<- | Peak grouping based on time dimension peak densities |
| minSamples<--method | Peak grouping based on time dimension peak densities |
| minSamples<--method | High resolution peak grouping for single spectra samples |
| mslevel | Class xcmsSet, a class for preprocessing peak data |
| msLevel-method | Tracking data processing |
| mslevel-method | Class xcmsRaw, a class for handling raw data |
| mslevel-method | Class xcmsSet, a class for preprocessing peak data |
| msn2xcmsRaw | Copy MSn data in an xcmsRaw to the MS slots |
| MSW | Single-spectrum non-chromatography MS data peak detection |
| MSWParam | Single-spectrum non-chromatography MS data peak detection |
| MSWParam-class | Single-spectrum non-chromatography MS data peak detection |
| mz,CalibrantMassParam | Calibrant mass based calibration of chromatgraphic peaks |
| mz-method | Data container storing xcms preprocessing results |
| mzCenterFun | Chromatographic peak detection using the centWave method |
| mzCenterFun-method | Chromatographic peak detection using the centWave method |
| mzCenterFun-method | Chromatographic peak detection using the massifquant method |
| mzCenterFun<- | Chromatographic peak detection using the centWave method |
| mzCenterFun<--method | Chromatographic peak detection using the centWave method |
| mzCenterFun<--method | Chromatographic peak detection using the massifquant method |
| MzClustParam | High resolution peak grouping for single spectra samples |
| MzClustParam-class | High resolution peak grouping for single spectra samples |
| mzdiff | Chromatographic peak detection using the centWave method |
| mzdiff-method | Chromatographic peak detection using the centWave method |
| mzdiff-method | Chromatographic peak detection using the massifquant method |
| mzdiff-method | Peak detection in the chromatographic time domain |
| mzdiff<- | Chromatographic peak detection using the centWave method |
| mzdiff<--method | Chromatographic peak detection using the centWave method |
| mzdiff<--method | Chromatographic peak detection using the massifquant method |
| mzdiff<--method | Peak detection in the chromatographic time domain |
| mzIntervalExtension | Two-step centWave peak detection considering also isotopes |
| mzIntervalExtension-method | Two-step centWave peak detection considering also isotopes |
| mzIntervalExtension<- | Two-step centWave peak detection considering also isotopes |
| mzIntervalExtension<--method | Two-step centWave peak detection considering also isotopes |
| mzrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
| mzrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
| mzVsRtBalance | Peak grouping based on proximity in the mz-rt space |
| mzVsRtBalance-method | Peak grouping based on proximity in the mz-rt space |
| mzVsRtBalance<- | Peak grouping based on proximity in the mz-rt space |
| mzVsRtBalance<--method | Peak grouping based on proximity in the mz-rt space |
| nearbyPeak | Single-spectrum non-chromatography MS data peak detection |
| nearbyPeak-method | Single-spectrum non-chromatography MS data peak detection |
| nearbyPeak<- | Single-spectrum non-chromatography MS data peak detection |
| nearbyPeak<--method | Single-spectrum non-chromatography MS data peak detection |
| NearestPeaksParam | Peak grouping based on proximity in the mz-rt space |
| NearestPeaksParam-class | Peak grouping based on proximity in the mz-rt space |
| noise | Chromatographic peak detection using the centWave method |
| noise-method | Chromatographic peak detection using the centWave method |
| noise-method | Chromatographic peak detection using the massifquant method |
| noise<- | Chromatographic peak detection using the centWave method |
| noise<--method | Chromatographic peak detection using the centWave method |
| noise<--method | Chromatographic peak detection using the massifquant method |
| normalize-Chromatogram | Normalize chromatographic data |
| normalize-method | XCMSnExp data manipulation methods inherited from MSnbase |
| normalize-method | Normalize chromatographic data |
| ObiwarpParam | Align retention times across samples using Obiwarp |
| ObiwarpParam-class | Align retention times across samples using Obiwarp |
| overlappingFeatures | Identify overlapping features |
| Param | Generic parameter class |
| Param-class | Generic parameter class |
| PeakDensityParam | Peak grouping based on time dimension peak densities |
| PeakDensityParam-class | Peak grouping based on time dimension peak densities |
| peakGroupsMatrix | Retention time correction based on alignment of house keeping peak groups |
| peakGroupsMatrix-method | Retention time correction based on alignment of house keeping peak groups |
| peakGroupsMatrix<- | Retention time correction based on alignment of house keeping peak groups |
| peakGroupsMatrix<--method | Retention time correction based on alignment of house keeping peak groups |
| PeakGroupsParam | Retention time correction based on alignment of house keeping peak groups |
| PeakGroupsParam-class | Retention time correction based on alignment of house keeping peak groups |
| peakPlots-method | Plot a grid of a large number of peaks |
| peakPlots-methods | Plot a grid of a large number of peaks |
| peaks | Class xcmsSet, a class for preprocessing peak data |
| peaks-method | Class xcmsSet, a class for preprocessing peak data |
| peaks<- | Class xcmsSet, a class for preprocessing peak data |
| peaks<--method | Class xcmsSet, a class for preprocessing peak data |
| peakScaleRange | Single-spectrum non-chromatography MS data peak detection |
| peakScaleRange-method | Single-spectrum non-chromatography MS data peak detection |
| peakScaleRange<- | Single-spectrum non-chromatography MS data peak detection |
| peakScaleRange<--method | Single-spectrum non-chromatography MS data peak detection |
| 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 |
| peakThr | Single-spectrum non-chromatography MS data peak detection |
| peakThr-method | Single-spectrum non-chromatography MS data peak detection |
| peakThr<- | Single-spectrum non-chromatography MS data peak detection |
| peakThr<--method | Single-spectrum non-chromatography MS data peak detection |
| peakwidth | Chromatographic peak detection using the centWave method |
| peakwidth-method | Chromatographic peak detection using the centWave method |
| peakwidth-method | Chromatographic peak detection using the massifquant method |
| peakwidth<- | Chromatographic peak detection using the centWave method |
| peakwidth<--method | Chromatographic peak detection using the centWave method |
| peakwidth<--method | Chromatographic peak detection using the massifquant method |
| phenoData | Class xcmsSet, a class for preprocessing peak data |
| phenoData-method | Class xcmsSet, a class for preprocessing peak data |
| phenoData<- | Class xcmsSet, a class for preprocessing peak data |
| phenoData<--method | Class xcmsSet, a class for preprocessing peak data |
| phenoDataFromPaths | Derive experimental design from file paths |
| pickPeaks-method | XCMSnExp data manipulation methods inherited from MSnbase |
| plot, plot-methods | Plot extracted ion chromatograms from multiple files |
| plot-method | Data container storing xcms preprocessing results |
| plot-method | Containers for chromatographic and peak detection data |
| 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 |
| 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 |
| 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 |
| plotQC | Plot m/z and RT deviations for QC purposes without external reference data |
| plotRaw | Scatterplot of raw data points |
| plotRaw-method | Scatterplot of raw data points |
| plotrt | Plot retention time deviation profiles |
| plotrt-method | Plot retention time deviation profiles |
| plotScan | Plot a single mass scan |
| plotScan-method | Plot a single mass scan |
| plotSpec | Plot mass spectra from the profile matrix |
| plotSpec-method | Plot mass spectra from the profile matrix |
| plotSurf | Plot profile matrix 3D surface using OpenGL |
| plotSurf-method | Plot profile matrix 3D surface using OpenGL |
| plotTIC | Plot total ion count |
| plotTIC-method | Plot total ion count |
| plotTree | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
| plotTree-method | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
| polarity-method | Two-step centWave peak detection considering also isotopes |
| polarity<- | Two-step centWave peak detection considering also isotopes |
| polarity<--method | Two-step centWave peak detection considering also isotopes |
| ppm | Chromatographic peak detection using the centWave method |
| ppm-method | Integrate areas of missing peaks |
| ppm-method | Chromatographic peak detection using the centWave method |
| ppm-method | Chromatographic peak detection using the massifquant method |
| ppm-method | High resolution peak grouping for single spectra samples |
| ppm<- | Chromatographic peak detection using the centWave method |
| ppm<--method | Integrate areas of missing peaks |
| ppm<--method | Chromatographic peak detection using the centWave method |
| ppm<--method | Chromatographic peak detection using the massifquant method |
| ppm<--method | High resolution peak grouping for single spectra samples |
| prefilter | Chromatographic peak detection using the centWave method |
| prefilter-method | Chromatographic peak detection using the centWave method |
| prefilter-method | Chromatographic peak detection using the massifquant method |
| prefilter<- | Chromatographic peak detection using the centWave method |
| prefilter<--method | Chromatographic peak detection using the centWave method |
| prefilter<--method | Chromatographic peak detection using the massifquant method |
| present | Determine which peaks are absent / present in a sample class |
| present-method | Determine which peaks are absent / present in a sample class |
| processDate | Tracking data processing |
| processDate-method | Tracking data processing |
| ProcessHistory | Tracking data processing |
| processHistory | Data container storing xcms preprocessing results |
| ProcessHistory-class | Tracking data processing |
| processHistory-method | Data container storing xcms preprocessing results |
| processHistory-method | Containers for chromatographic and peak detection data |
| 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-method | Accessing mz-rt feature data values |
| 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 |
| refineChromPeaks | Remove chromatographic peaks with too large rt width |
| refineChromPeaks-method | Containers for chromatographic and peak detection data |
| refineChromPeaks-method | Remove chromatographic peaks with too large rt width |
| refineChromPeaks-method | Remove chromatographic peaks based on intensity |
| refineChromPeaks-method | Merge neighboring and overlapping chromatographic peaks |
| removeIntensity | Remove intensities from chromatographic data |
| removeIntensity-method | Remove intensities from chromatographic data |
| removePeaks-method | XCMSnExp data manipulation methods inherited from MSnbase |
| response | Align retention times across samples using Obiwarp |
| response-method | Align retention times across samples using Obiwarp |
| response<- | Align retention times across samples using Obiwarp |
| response<--method | Align retention times across samples using Obiwarp |
| retcor | Correct retention time from different samples |
| retcor-method | Correct retention time from different samples |
| retcor-methods | Correct retention time from different samples |
| retcor.linear | Align retention times across samples |
| retcor.linear-method | Align retention times across samples |
| retcor.loess | Align retention times across samples |
| retcor.loess-method | Align retention times across samples |
| retcor.obiwarp | Align retention times across samples with Obiwarp |
| retcor.obiwarp-method | Align retention times across samples with Obiwarp |
| retcor.peakgroups | Align retention times across samples |
| retcor.peakgroups-method | Align retention times across samples |
| retexp | Set retention time window to a specified width |
| revMz | Class xcmsRaw, a class for handling raw data |
| revMz-method | Class xcmsRaw, a class for handling raw data |
| ridgeLength | Single-spectrum non-chromatography MS data peak detection |
| ridgeLength-method | Single-spectrum non-chromatography MS data peak detection |
| ridgeLength<- | Single-spectrum non-chromatography MS data peak detection |
| ridgeLength<--method | Single-spectrum non-chromatography MS data peak detection |
| rla | Calculate relative log abundances 'rla' calculates the relative log abundances (RLA, see reference) on a 'numeric' vector. |
| roiList | Chromatographic peak detection using the centWave method |
| roiList-method | Chromatographic peak detection using the centWave method |
| roiList<- | Chromatographic peak detection using the centWave method |
| roiList<--method | Chromatographic peak detection using the centWave method |
| roiScales | Chromatographic peak detection using the centWave method |
| roiScales-method | Chromatographic peak detection using the centWave method |
| roiScales<- | Chromatographic peak detection using the centWave method |
| roiScales<--method | Chromatographic peak detection using the centWave method |
| rowRla | Calculate relative log abundances 'rla' calculates the relative log abundances (RLA, see reference) on a 'numeric' vector. |
| rtime-method | Data container storing xcms preprocessing results |
| rtrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
| rtrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
| sampclass | Class xcmsSet, a class for preprocessing peak data |
| sampclass-method | Class xcmsSet, a class for preprocessing peak data |
| sampclass<- | Class xcmsSet, a class for preprocessing peak data |
| sampclass<--method | Class xcmsSet, a class for preprocessing peak data |
| sampleGroups | Peak grouping based on time dimension peak densities |
| sampleGroups-method | Peak grouping based on time dimension peak densities |
| sampleGroups-method | High resolution peak grouping for single spectra samples |
| sampleGroups-method | Peak grouping based on proximity in the mz-rt space |
| sampleGroups<- | Peak grouping based on time dimension peak densities |
| sampleGroups<--method | Peak grouping based on time dimension peak densities |
| sampleGroups<--method | High resolution peak grouping for single spectra samples |
| sampleGroups<--method | Peak grouping based on proximity in the mz-rt space |
| sampnames | Get sample names |
| sampnames-method | Get sample names |
| sampnames<- | Class xcmsSet, a class for preprocessing peak data |
| sampnames<--method | Class xcmsSet, a class for preprocessing peak data |
| scales | Single-spectrum non-chromatography MS data peak detection |
| scales-method | Single-spectrum non-chromatography MS data peak detection |
| scales<- | Single-spectrum non-chromatography MS data peak detection |
| scales<--method | Single-spectrum non-chromatography MS data peak detection |
| scanrange | Class xcmsSet, a class for preprocessing peak data |
| scanrange-method | Class xcmsRaw, a class for handling raw data |
| scanrange-method | Class xcmsSet, a class for preprocessing peak data |
| setAs | Data container storing xcms preprocessing results |
| show-method | Generic parameter class |
| show-method | Tracking data processing |
| show-method | Data container storing xcms preprocessing results |
| show-method | Containers for chromatographic and peak detection data |
| show-method | Align retention times across samples using Obiwarp |
| show-method | Retention time correction based on alignment of house keeping peak groups |
| show-method | Integrate areas of missing peaks |
| show-method | Chromatographic peak detection using the centWave method |
| show-method | Two-step centWave peak detection considering also isotopes |
| show-method | Chromatographic peak detection using the massifquant method |
| show-method | Peak detection in the chromatographic time domain |
| show-method | Single-spectrum non-chromatography MS data peak detection |
| show-method | Peak grouping based on time dimension peak densities |
| show-method | High resolution peak grouping for single spectra samples |
| show-method | Peak grouping based on proximity in the mz-rt space |
| show-method | Remove chromatographic peaks with too large rt width |
| show-method | Remove chromatographic peaks based on intensity |
| show-method | Merge neighboring and overlapping chromatographic peaks |
| show-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
| show-method | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
| show-method | A matrix of peaks |
| show-method | Class xcmsRaw, a class for handling raw data |
| show-method | Class xcmsSet, a class for preprocessing peak data |
| showError | Extract processing errors |
| showError-method | Extract processing errors |
| sigma | Peak detection in the chromatographic time domain |
| sigma-method | Peak detection in the chromatographic time domain |
| sigma<- | Peak detection in the chromatographic time domain |
| sigma<--method | Peak detection in the chromatographic time domain |
| smooth | Retention time correction based on alignment of house keeping peak groups |
| smooth-method | XCMSnExp data manipulation methods inherited from MSnbase |
| smooth-method | Retention time correction based on alignment of house keeping peak groups |
| smooth<- | Retention time correction based on alignment of house keeping peak groups |
| smooth<--method | Retention time correction based on alignment of house keeping peak groups |
| snthresh | Chromatographic peak detection using the centWave method |
| snthresh-method | Chromatographic peak detection using the centWave method |
| snthresh-method | Chromatographic peak detection using the massifquant method |
| snthresh-method | Peak detection in the chromatographic time domain |
| snthresh-method | Single-spectrum non-chromatography MS data peak detection |
| snthresh<- | Chromatographic peak detection using the centWave method |
| snthresh<--method | Chromatographic peak detection using the centWave method |
| snthresh<--method | Chromatographic peak detection using the massifquant method |
| snthresh<--method | Peak detection in the chromatographic time domain |
| snthresh<--method | Single-spectrum non-chromatography MS data peak detection |
| snthreshIsoROIs | Two-step centWave peak detection considering also isotopes |
| snthreshIsoROIs-method | Two-step centWave peak detection considering also isotopes |
| snthreshIsoROIs<- | Two-step centWave peak detection considering also isotopes |
| snthreshIsoROIs<--method | Two-step centWave peak detection considering also isotopes |
| sortMz | Class xcmsRaw, a class for handling raw data |
| sortMz-method | Class xcmsRaw, a class for handling raw data |
| span | Retention time correction based on alignment of house keeping peak groups |
| span-method | Retention time correction based on alignment of house keeping peak groups |
| span<- | Retention time correction based on alignment of house keeping peak groups |
| span<--method | Retention time correction based on alignment of house keeping peak groups |
| specDist | Distance methods for xcmsSet, xcmsRaw and xsAnnotate |
| specDist-method | Distance methods for xcmsSet, xcmsRaw and xsAnnotate |
| specDist-methods | Distance methods for xcmsSet, xcmsRaw and xsAnnotate |
| specDist.cosine | a Distance function based on matching peaks |
| specDist.cosine-method | a Distance function based on matching peaks |
| specDist.meanMZmatch | a Distance function based on matching peaks |
| specDist.meanMZmatch-method | a Distance function based on matching peaks |
| specDist.peakCount | a Distance function based on matching peaks |
| specDist.peakCount-method | a Distance function based on matching peaks |
| specDist.peakCount-methods | a Distance function based on matching peaks |
| specNoise | Calculate noise for a sparse continuum mass spectrum |
| specPeaks | Identify peaks in a sparse continuum mode spectrum |
| spectra-method | Data container storing xcms preprocessing results |
| spectrapply-method | Data container storing xcms preprocessing results |
| split, split-methods | Divide an xcmsSet object |
| split-method | XCMSnExp filtering and subsetting |
| split.xcmsRaw | Divide an xcmsRaw object |
| split.xcmsSet | Divide an xcmsSet object |
| SSgauss | Gaussian Model |
| steps | Peak detection in the chromatographic time domain |
| steps-method | Peak detection in the chromatographic time domain |
| steps<- | Peak detection in the chromatographic time domain |
| steps<--method | Peak detection in the chromatographic time domain |
| stitch | Correct gaps in data |
| stitch-method | Correct gaps in data |
| stitch-methods | Correct gaps in data |
| stitch.netCDF | Correct gaps in data |
| stitch.xml | Correct gaps in data |
| subset | Retention time correction based on alignment of house keeping peak groups |
| subset-method | Align retention times across samples using Obiwarp |
| subset-method | Retention time correction based on alignment of house keeping peak groups |
| subset-xcmsRaw | Subset an xcmsRaw object by scans |
| subset<- | Retention time correction based on alignment of house keeping peak groups |
| subset<--method | Align retention times across samples using Obiwarp |
| subset<--method | Retention time correction based on alignment of house keeping peak groups |
| subsetAdjust | Retention time correction based on alignment of house keeping peak groups |
| subsetAdjust-method | Align retention times across samples using Obiwarp |
| subsetAdjust-method | Retention time correction based on alignment of house keeping peak groups |
| subsetAdjust<- | Retention time correction based on alignment of house keeping peak groups |
| subsetAdjust<--method | Align retention times across samples using Obiwarp |
| subsetAdjust<--method | Retention time correction based on alignment of house keeping peak groups |
| tuneIn | Single-spectrum non-chromatography MS data peak detection |
| tuneIn-method | Single-spectrum non-chromatography MS data peak detection |
| tuneIn<- | Single-spectrum non-chromatography MS data peak detection |
| tuneIn<--method | Single-spectrum non-chromatography MS data peak detection |
| unions | Chromatographic peak detection using the massifquant method |
| unions-method | Chromatographic peak detection using the massifquant method |
| unions<- | Chromatographic peak detection using the massifquant method |
| unions<--method | Chromatographic peak detection using the massifquant method |
| updateObject-method | Data container storing xcms preprocessing results |
| updateObject-method | Update an 'xcmsSet' object |
| useOriginalCode | Enable usage of old xcms code |
| verboseColumns | Chromatographic peak detection using the centWave method |
| verboseColumns-method | Chromatographic peak detection using the centWave method |
| verboseColumns-method | Chromatographic peak detection using the massifquant method |
| verboseColumns-method | Single-spectrum non-chromatography MS data peak detection |
| verboseColumns<- | Chromatographic peak detection using the centWave method |
| verboseColumns<--method | Chromatographic peak detection using the centWave method |
| verboseColumns<--method | Chromatographic peak detection using the massifquant method |
| verboseColumns<--method | Single-spectrum non-chromatography MS data peak detection |
| verify.mzQuantML | Verify an mzQuantML file |
| withWave | Chromatographic peak detection using the massifquant method |
| withWave-method | Chromatographic peak detection using the massifquant method |
| withWave<- | Chromatographic peak detection using the massifquant method |
| withWave<--method | Chromatographic peak detection using the massifquant method |
| write.cdf | Save an xcmsRaw object to file |
| write.cdf-method | Save an xcmsRaw object to file |
| write.mzdata | Save an xcmsRaw object to a file |
| write.mzdata-method | Save an xcmsRaw object to a file |
| write.mzQuantML | Save an xcmsSet object to an PSI mzQuantML file |
| write.mzQuantML-method | Save an xcmsSet object to an PSI mzQuantML file |
| 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 |
| 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 |
| 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 | Subset an xcmsRaw object by scans |
| [-method | Class xcmsSet, a class for preprocessing peak data |
| [[-method | XCMSnExp filtering and subsetting |