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"adjustRtime,XCMSnExp,ObiwarpParam-method", "adjustRtime,XCMSnExp,PeakGroupsParam-method", "adjustRtimePeakGroups", "binSize<-,ObiwarpParam-method", "ObiwarpParam", "PeakGroupsParam" ] }, { "page": "LamaParama", "title": "Landmark-based alignment: aligning a dataset against an external reference", "topics": [ "adjustRtime,XcmsExperiment,LamaParama-method", "LamaParama", "LamaParama-class", "matchedRtimes", "matchLamasChromPeaks", "plot,LamaParama,ANY-method", "summarizeLamaMatch" ] }, { "page": "applyAdjustedRtime", "title": "Replace raw with adjusted retention times", "topics": [ "applyAdjustedRtime" ] }, { "page": "AutoLockMass-methods", "title": "Automatic parameter for Lock mass fixing 'AutoLockMass' ~~", "topics": [ "AutoLockMass", "AutoLockMass,xcmsRaw-method", "AutoLockMass-methods" ] }, { "page": "XCMSnExp-inherited-methods", "title": "XCMSnExp data manipulation methods inherited from MSnbase", "topics": [ "bin,XCMSnExp-method", "clean,XCMSnExp-method", "filterAcquisitionNum,XCMSnExp-method", "normalize,XCMSnExp-method", "pickPeaks,XCMSnExp-method", "removePeaks,XCMSnExp-method", "smooth,XCMSnExp-method" ] }, { "page": "binYonX", "title": "Aggregate values in y for bins defined on x", "topics": [ "binYonX" ] }, { "page": "BlankFlag", "title": "Flag features based on the intensity in blank samples", "concept": [ "Filter features in xcms" ], "topics": [ "BlankFlag", "filterFeatures,SummarizedExperiment,BlankFlag-method", "filterFeatures,XcmsResult,BlankFlag-method" ] }, { "page": "breaks_on_binSize", "title": "Generate breaks for binning using a defined bin size.", "concept": [ "functions to define bins" ], "topics": [ "breaks_on_binSize" ] }, { "page": "breaks_on_nBins", "title": "Generate breaks for binning", "concept": [ "functions to define bins" ], "topics": [ "breaks_on_nBins" ] }, { "page": "c.xcmsSet", "title": "Combine xcmsSet objects", "topics": [ "c, c-methods", "c.xcmsSet" ] }, { "page": "calibrate-calibrant-mass", "title": "Calibrant mass based calibration of chromatgraphic peaks", "topics": [ "CalibrantMassParam", "CalibrantMassParam-class", "calibrate,XCMSnExp-method", "isCalibrated", "mz,CalibrantMassParam" ] }, { "page": "calibrate", "title": "Calibrate peaks for correcting unprecise m/z values", "topics": [ "calibrate", "calibrate,xcmsSet-method" ] }, { "page": "chromatogram-method", "title": "Extracting chromatograms", "topics": [ "chromatogram", "chromatogram,XCMSnExp-method" ] }, { "page": "chromPeakChromatograms", "title": "Extract an ion chromatogram for each chromatographic peak", "topics": [ "chromPeakChromatograms", "chromPeakChromatograms,XcmsExperiment-method" ] }, { "page": "chromPeakSpectra", "title": "Extract spectra associated with chromatographic peaks", "topics": [ "chromPeakSpectra", "chromPeakSpectra,XcmsExperiment-method", "chromPeakSpectra,XCMSnExp-method" ] }, { "page": "chromPeakSummary", "title": "Chromatographic peak summaries", "topics": [ "BetaDistributionParam", "chromPeakSummary", "chromPeakSummary,XcmsExperiment,BetaDistributionParam-method" ] }, { "page": "collect-methods", "title": "Collect MS^n peaks into xcmsFragments", "topics": [ "collect", "collect,xcmsFragments-method", "collect,xcmsRaw-method", "collect-methods" ] }, { "page": "correlate-Chromatogram", "title": "Correlate chromatograms", "topics": [ "correlate", "correlate,Chromatogram,Chromatogram-method", "correlate,MChromatograms,MChromatograms-method", "correlate,MChromatograms,missing-method" ] }, { "page": "diffreport-methods", "title": "Create report of analyte differences", "topics": [ "diffreport", "diffreport,xcmsSet-method" ] }, { "page": "dirname", "title": "Change the file path of an 'OnDiskMSnExp' object", "topics": [ "dirname", "dirname,OnDiskMSnExp-method", "dirname<-,OnDiskMSnExp-method" ] }, { "page": "do_adjustRtime_peakGroups", "title": "Align spectrum retention times across samples using peak groups found in most samples", "concept": [ "core retention time correction algorithms" ], "topics": [ "do_adjustRtime_peakGroups" ] }, { "page": "do_findChromPeaks_centWave", "title": "Core API function for centWave peak detection", "concept": [ "core peak detection functions" ], "topics": [ "do_findChromPeaks_centWave" ] }, { "page": "do_findChromPeaks_centWaveWithPredIsoROIs", "title": "Core API function for two-step centWave peak detection with isotopes", "concept": [ "core peak detection functions" ], "topics": [ "do_findChromPeaks_addPredIsoROIs", "do_findChromPeaks_centWaveWithPredIsoROIs" ] }, { "page": "do_findChromPeaks_massifquant", "title": "Core API function for massifquant peak detection", "concept": [ "core peak detection functions" ], "topics": [ "do_findChromPeaks_massifquant" ] }, { "page": "do_findChromPeaks_matchedFilter", "title": "Core API function for matchedFilter peak detection", "concept": [ "core peak detection functions" ], "topics": [ "do_findChromPeaks_matchedFilter" ] }, { "page": "do_findPeaks_MSW", "title": "Core API function for single-spectrum non-chromatography MS data peak detection", "concept": [ "core peak detection functions" ], "topics": [ "do_findPeaks_MSW" ] }, { "page": "do_groupChromPeaks_density", "title": "Core API function for peak density based chromatographic peak grouping", "concept": [ "core peak grouping algorithms" ], "topics": [ "do_groupChromPeaks_density" ] }, { "page": "do_groupChromPeaks_nearest", "title": "Core API function for chromatic peak grouping using a nearest neighbor approach", "concept": [ "core peak grouping algorithms" ], "topics": [ "do_groupChromPeaks_nearest" ] }, { "page": "do_groupPeaks_mzClust", "title": "Core API function for peak grouping using mzClust", "concept": [ "core peak grouping algorithms" ], "topics": [ "do_groupPeaks_mzClust" ] }, { "page": "DratioFilter", "title": "Filter features based on the dispersion ratio", "concept": [ "Filter features in xcms" ], "topics": [ "DratioFilter", "filterFeatures,SummarizedExperiment,DratioFilter-method", "filterFeatures,XcmsResult,DratioFilter-method" ] }, { "page": "estimatePrecursorIntensity", "title": "Estimate precursor intensity for MS level 2 spectra", "topics": [ "estimatePrecursorIntensity,MsExperiment-method", "estimatePrecursorIntensity,OnDiskMSnExp-method" ] }, { "page": "etg", "title": "Empirically Transformed Gaussian function", "topics": [ "etg" ] }, { "page": "exportMetaboAnalyst", "title": "Export data for use in MetaboAnalyst", "topics": [ "exportMetaboAnalyst" ] }, { "page": "extractMsData-method", "title": "DEPRECATED: Extract a 'data.frame' containing MS data", "topics": [ "extractMsData", "extractMsData,OnDiskMSnExp-method", "extractMsData,XCMSnExp-method" ] }, { "page": "feature-grouping", "title": "Compounding of LC-MS features", "topics": [ "feature-grouping", "featureGroups,XcmsResult-method", "featureGroups<-,XcmsResult-method" ] }, { "page": "featureChromatograms", "title": "Extract ion chromatograms for each feature", "topics": [ "featureChromatograms", "featureChromatograms,XcmsExperiment-method", "featureChromatograms,XCMSnExp-method" ] }, { "page": "featureSpectra", "title": "Extract spectra associated with features", "topics": [ "featureSpectra", "featureSpectra,XcmsExperiment-method", "featureSpectra,XCMSnExp-method" ] }, { "page": "featureSummary", "title": "Simple feature summaries", "topics": [ "featureSummary" ] }, { "page": "fillChromPeaks", "title": "Gap Filling", "topics": [ "ChromPeakAreaParam", "fillChromPeaks", "fillChromPeaks,XcmsExperiment,ChromPeakAreaParam-method", "fillChromPeaks,XCMSnExp,ChromPeakAreaParam-method", "fillChromPeaks,XCMSnExp,FillChromPeaksParam-method", "fillChromPeaks,XCMSnExp,missing-method", "FillChromPeaksParam" ] }, { "page": "fillPeaks-methods", "title": "Integrate areas of missing peaks", "topics": [ "fillPeaks", "fillPeaks,xcmsSet-method" ] }, { "page": "fillPeaks.chrom-methods", "title": "Integrate areas of missing peaks", "topics": [ "fillPeaks.chrom", "fillPeaks.chrom,xcmsSet-method" ] }, { "page": "fillPeaks.MSW-methods", "title": "Integrate areas of missing peaks in FTICR-MS data", "topics": [ "fillPeaks.MSW", "fillPeaks.MSW,xcmsSet-method" ] }, { "page": "filter-MChromatograms", "title": "Filtering sets of chromatographic data", "topics": [ "filterColumnsIntensityAbove", "filterColumnsIntensityAbove,MChromatograms-method", "filterColumnsIntensityAbove,XChromatograms-method", "filterColumnsKeepTop", "filterColumnsKeepTop,MChromatograms-method", "filterColumnsKeepTop,XChromatograms-method" ] }, { "page": "XcmsExperiment", "title": "Next Generation 'xcms' Result Object", "topics": [ "adjustedRtime,XcmsExperiment-method", "c.XcmsExperiment", "chromatogram,MsExperiment-method", "chromatogram,XcmsExperiment-method", "chromPeakData,XcmsExperiment-method", "chromPeakData<-,XcmsExperiment-method", "chromPeaks,XcmsExperiment-method", "chromPeaks<-,XcmsExperiment-method", "dropAdjustedRtime,XcmsExperiment-method", "dropChromPeaks,XcmsExperiment-method", "dropFeatureDefinitions,XcmsExperiment-method", "dropFilledChromPeaks,XcmsExperiment-method", "featureArea", "featureArea,XcmsResult-method", "featureDefinitions,XcmsExperiment-method", "featureDefinitions<-,XcmsExperiment-method", "featureValues,XcmsExperiment-method", "fileNames,MsExperiment-method", "filterChromPeaks", "filterChromPeaks,XcmsExperiment-method", "filterFeatureDefinitions", "filterFeatureDefinitions,XcmsExperiment-method", "filterFile,MsExperiment-method", "filterFile,XcmsExperiment-method", "filterIsolationWindow,MsExperiment-method", "filterIsolationWindow,XcmsExperiment-method", "filterMsLevel,MsExperiment-method", "filterMsLevel,XcmsExperiment-method", "filterMz,MsExperiment-method", "filterMzRange,MsExperiment-method", "filterMzRange,XcmsExperiment-method", "filterRt,MsExperiment-method", "filterRt,XcmsExperiment-method", "fromFile,MsExperiment-method", "hasAdjustedRtime,MsExperiment-method", "hasChromPeaks,XcmsExperiment-method", "hasFeatures,XcmsExperiment-method", "hasFilledChromPeaks,XcmsExperiment-method", "plot,MsExperiment,missing-method", "polarity,MsExperiment-method", "processHistory,XcmsExperiment-method", "quantify", "quantify,XcmsExperiment-method", "rtime,MsExperiment-method", "rtime,XcmsExperiment-method", "uniqueMsLevels,MsExperiment-method", "XcmsExperiment", "XcmsExperiment-class", "[,XcmsExperiment,ANY,ANY,ANY-method" ] }, { "page": "filterFeatures", "title": "Filtering of features based on conventional quality assessment", "topics": [ "filterFeatures" ] }, { "page": "findChromPeaks", "title": "Chromatographic Peak Detection", "concept": [ "peak detection methods" ], "topics": [ "findChromPeaks", "findChromPeaks,MsExperiment,Param-method", "findChromPeaks,XcmsExperiment,Param-method" ] }, { "page": "findChromPeaks-centWave", "title": "Chromatographic peak detection using the centWave method", "concept": [ "peak detection methods" ], "topics": [ "as.list,CentWaveParam-method", "centWave", "CentWaveParam", "findChromPeaks,OnDiskMSnExp,CentWaveParam-method", "findChromPeaks-centWave" ] }, { "page": "findChromPeaks-centWaveWithPredIsoROIs", "title": "Two-step centWave peak detection considering also isotopes", "concept": [ "peak detection methods" ], "topics": [ "CentWavePredIsoParam", "centWaveWithPredIsoROIs", "findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam-method", "findChromPeaks-centWaveWithPredIsoROIs" ] }, { "page": "findChromPeaks-massifquant", "title": "Chromatographic peak detection using the massifquant method", "concept": [ "peak detection methods" ], "topics": [ "findChromPeaks,OnDiskMSnExp,MassifquantParam-method", "findChromPeaks-massifquant", "massifquant", "MassifquantParam" ] }, { "page": "findChromPeaks-matchedFilter", "title": "Peak detection in the chromatographic time domain", "concept": [ "peak detection methods" ], "topics": [ "findChromPeaks,OnDiskMSnExp,MatchedFilterParam-method", "findChromPeaks-matchedFilter", "matchedFilter", "MatchedFilterParam" ] }, { "page": "findChromPeaks-Chromatogram-CentWaveParam", "title": "centWave-based peak detection in purely chromatographic data", "topics": [ "findChromPeaks,Chromatogram,CentWaveParam-method", "findChromPeaks,MChromatograms,CentWaveParam-method", "findChromPeaks,MChromatograms,MatchedFilterParam-method", "findChromPeaks-Chromatogram-CentWaveParam" ] }, { "page": "findChromPeaks-Chromatogram-MatchedFilter", "title": "matchedFilter-based peak detection in purely chromatographic data", "topics": [ "findChromPeaks,Chromatogram,MatchedFilterParam-method" ] }, { "page": "findChromPeaksIsolationWindow", "title": "Data independent acquisition (DIA): peak detection in isolation windows", "topics": [ "findChromPeaksIsolationWindow", "findChromPeaksIsolationWindow,MsExperiment-method", "findChromPeaksIsolationWindow,OnDiskMSnExp-method" ] }, { "page": "findMZ", "title": "Find fragment ions in xcmsFragment objects", "topics": [ "findMZ", "findMZ,xcmsFragments-method" ] }, { "page": "findneutral", "title": "Find neutral losses in xcmsFragment objects", "topics": [ "findneutral", "findneutral,xcmsFragments-method" ] }, { "page": "findPeaks-methods", "title": "Feature detection for GC/MS and LC/MS Data - methods", "topics": [ "findPeaks", "findPeaks,xcmsRaw-method", "findPeaks-methods" ] }, { "page": "findPeaks-MSW", "title": "Single-spectrum non-chromatography MS data peak detection", "concept": [ "peak detection methods" ], "topics": [ "findChromPeaks,OnDiskMSnExp,MSWParam-method", "findPeaks-MSW", "MSW", "MSWParam" ] }, { "page": "findPeaks.addPredictedIsotopeFeatures-methods", "title": "Feature detection based on predicted isotope features for high resolution LC/MS data", "topics": [ "findPeaks.addPredictedIsotopeFeatures", "findPeaks.addPredictedIsotopeFeatures,xcmsRaw-method" ] }, { "page": "findPeaks.centWave-methods", "title": "Feature detection for high resolution LC/MS data", "topics": [ "findPeaks.centWave", "findPeaks.centWave,xcmsRaw-method" ] }, { "page": "findPeaks.centWaveWithPredictedIsotopeROIs-methods", "title": "Feature detection with centWave and additional isotope features", "topics": [ "findPeaks.centWaveWithPredictedIsotopeROIs", "findPeaks.centWaveWithPredictedIsotopeROIs,xcmsRaw-method" ] }, { "page": "findPeaks.massifquant-methods", "title": "Feature detection for XC-MS data.", "topics": [ "findPeaks.massifquant", "findPeaks.massifquant,xcmsRaw-method" ] }, { "page": "findPeaks.matchedFilter-xcmsRaw-method", "title": "Peak detection in the chromatographic time domain", "concept": [ "Old peak detection methods" ], "topics": [ "findPeaks.matchedFilter", "findPeaks.matchedFilter,xcmsRaw-method" ] }, { "page": "findPeaks.MS1-methods", "title": "Collecting MS1 precursor peaks", "topics": [ "findPeaks.MS1", "findPeaks.MS1,xcmsRaw-method" ] }, { "page": "findPeaks.MSW-xcmsRaw-method", "title": "Peak detection for single-spectrum non-chromatography MS data", "topics": [ "findPeaks.MSW", "findPeaks.MSW,xcmsRaw-method" ] }, { "page": "GenericParam", "title": "Generic parameter class", "topics": [ "GenericParam", "GenericParam-class", "Param" ] }, { "page": "getEIC-methods", "title": "Get extracted ion chromatograms for specified m/z ranges", "topics": [ "getEIC", "getEIC,xcmsRaw-method", "getEIC,xcmsSet-method" ] }, { "page": "getPeaks-methods", "title": "Get peak intensities for specified regions", "topics": [ "getPeaks", "getPeaks,xcmsRaw-method" ] }, { "page": "getScan-methods", "title": "Get m/z and intensity values for a single mass scan", "topics": [ "getMsnScan", "getMsnScan,xcmsRaw-method", "getScan", "getScan,xcmsRaw-method" ] }, { "page": "getSpec-methods", "title": "Get average m/z and intensity values for multiple mass scans", "topics": [ "getSpec", "getSpec,xcmsRaw-method" ] }, { "page": "getXcmsRaw-methods", "title": "Load the raw data for one or more files in the xcmsSet", "topics": [ "getXcmsRaw", "getXcmsRaw,xcmsSet-method" ] }, { "page": "group-methods", "title": "Group peaks from different samples together", "topics": [ "group", "group,xcmsSet-method", "group-methods" ] }, { "page": "group.density", "title": "Group peaks from different samples together", "topics": [ "group.density", "group.density,xcmsSet-method" ] }, { "page": "group.mzClust", "title": "Group Peaks via High Resolution Alignment", "topics": [ "group.mzClust", "group.mzClust,xcmsSet-method" ] }, { "page": "group.nearest", "title": "Group peaks from different samples together", "topics": [ "group.nearest", "group.nearest,xcmsSet-method" ] }, { "page": "groupChromPeaks", "title": "Correspondence: group chromatographic peaks across samples", "concept": [ "peak grouping methods" ], "topics": [ "as.list,PeakDensityParam-method", "groupChromPeaks", "groupChromPeaks,XcmsExperiment,Param-method", "groupChromPeaks,XCMSnExp,MzClustParam-method", "groupChromPeaks,XCMSnExp,NearestPeaksParam-method", "groupChromPeaks,XCMSnExp,PeakDensityParam-method", "MzClustParam", "NearestPeaksParam", "PeakDensityParam" ] }, { "page": "groupFeatures-abundance-correlation", "title": "Compounding/feature grouping based on similarity of abundances across samples", "concept": [ "feature grouping methods" ], "topics": [ "groupFeatures,XcmsResult,AbundanceSimilarityParam-method", "groupFeatures-abundance-correlation" ] }, { "page": "groupFeatures-eic-similarity", "title": "Compounding/feature grouping based on similarity of extracted ion chromatograms", "concept": [ "feature grouping methods" ], "topics": [ "EicSimilarityParam", "EicSimilarityParam-class", "groupFeatures,XcmsResult,EicSimilarityParam-method", "groupFeatures-eic-similarity" ] }, { "page": "groupFeatures-similar-rtime", "title": "Compounding/feature grouping based on similar retention times", "concept": [ "feature grouping methods" ], "topics": [ "groupFeatures,XcmsResult,SimilarRtimeParam-method", "groupFeatures-similar-rtime" ] }, { "page": "groupnames-methods", "title": "Generate unque names for peak groups", "topics": [ "groupnames", "groupnames,xcmsEIC-method", "groupnames,xcmsSet-method" ] }, { "page": "groupnames-XCMSnExp", "title": "Generate unique group (feature) names based on mass and retention time", "topics": [ "groupnames,XCMSnExp-method" ] }, { "page": "groupOverlaps", "title": "Group overlapping ranges", "topics": [ "groupOverlaps" ] }, { "page": "groupval-methods", "title": "Extract a matrix of peak values for each group", "topics": [ "groupval", "groupval,xcmsSet-method" ] }, { "page": "highlightChromPeaks", "title": "Add definition of chromatographic peaks to an extracted chromatogram plot", "topics": [ "highlightChromPeaks" ] }, { "page": "image.xcmsRaw", "title": "Plot log intensity image of a xcmsRaw object", "topics": [ "image,xcmsRaw-method" ] }, { "page": "imputeLinInterpol", "title": "Impute values for empty elements in a vector using linear interpolation", "topics": [ "imputeLinInterpol" ] }, { "page": "imputeRowMin", "title": "Replace missing values with a proportion of the row minimum", "concept": [ "imputation functions" ], "topics": [ "imputeRowMin" ] }, { "page": "imputeRowMinRand", "title": "Impute missing values with random numbers based on the row minimum", "concept": [ "imputation functions" ], "topics": [ "imputeRowMinRand" ] }, { "page": "isolationWindowTargetMz-OnDiskMSnExp-method", "title": "Extract isolation window target m/z definition", "topics": [ "isolationWindowTargetMz", "isolationWindowTargetMz,OnDiskMSnExp-method" ] }, { "page": "levelplot.xcmsRaw", "title": "Plot log intensity image of a xcmsRaw object", "topics": [ "levelplot,xcmsRaw-method", "levelplot,xcmsSet-method" ] }, { "page": "loadRaw-methods", "title": "Read binary data from a source", "topics": [ "loadRaw", "loadRaw,xcmsFileSource-method", "loadRaw,xcmsSource-method", "loadRaw-methods" ] }, { "page": "loadXcmsData", "title": "LC-MS preprocessing result test data sets", "topics": [ "faahko_sub", "faahko_sub2", "loadXcmsData", "xdata", "xmse" ] }, { "page": "manualChromPeaks", "title": "Manual peak integration and feature definition", "topics": [ "manualChromPeaks", "manualChromPeaks,MsExperiment-method", "manualChromPeaks,OnDiskMSnExp-method", "manualChromPeaks,XcmsExperiment-method", "manualChromPeaks,XCMSnExp-method", "manualFeatures", "manualFeatures,XcmsExperiment-method", "manualFeatures,XCMSnExp-method" ] }, { "page": "medianFilter", "title": "Apply a median filter to a matrix", "topics": [ "medianFilter" ] }, { "page": "msn2xcmsRaw", "title": "Copy MSn data in an xcmsRaw to the MS slots", "topics": [ "msn2xcmsRaw" ] }, { "page": "overlappingFeatures", "title": "Identify overlapping features", "topics": [ "overlappingFeatures" ] }, { "page": "peakPlots-methods", "title": "Plot a grid of a large number of peaks", "topics": [ "peakPlots,xcmsSet-method", "peakPlots-methods" ] }, { "page": "peaksWithCentWave", "title": "Identify peaks in chromatographic data using centWave", "concept": [ "peak detection functions for chromatographic data" ], "topics": [ "peaksWithCentWave" ] }, { "page": "peaksWithMatchedFilter", "title": "Identify peaks in chromatographic data using matchedFilter", "concept": [ "peak detection functions for chromatographic data" ], "topics": [ "peaksWithMatchedFilter" ] }, { "page": "peakTable-methods", "title": "Create report of aligned peak intensities", "topics": [ "peakTable", "peakTable,xcmsSet-method" ] }, { "page": "PercentMissingFilter", "title": "Filter features based on the percentage of missing data", "concept": [ "Filter features in xcms" ], "topics": [ "filterFeatures,SummarizedExperiment,PercentMissingFilter-method", "filterFeatures,XcmsResult,PercentMissingFilter-method", "PercentMissingFilter" ] }, { "page": "phenoDataFromPaths", "title": "Derive experimental design from file paths", "topics": [ "phenoDataFromPaths" ] }, { "page": "plot.xcmsEIC", "title": "Plot extracted ion chromatograms from multiple files", "topics": [ "plot, plot-methods", "plot.xcmsEIC" ] }, { "page": "plotAdjustedRtime", "title": "Visualization of Alignment Results", "topics": [ "plotAdjustedRtime" ] }, { "page": "plotChrom-methods", "title": "Plot extracted ion chromatograms from the profile matrix", "topics": [ "plotChrom", "plotChrom,xcmsRaw-method" ] }, { "page": "plotChromatogramsOverlay", "title": "Plot multiple chromatograms into the same plot", "topics": [ "plotChromatogramsOverlay", "plotChromatogramsOverlay,MChromatograms-method", "plotChromatogramsOverlay,XChromatograms-method" ] }, { "page": "plotChromPeakDensity", "title": "Plot chromatographic peak density along the retention time axis", "topics": [ "plotChromPeakDensity", "plotChromPeakDensity,XCMSnExp-method" ] }, { "page": "plotChromPeaks", "title": "General visualizations of peak detection results", "topics": [ "plotChromPeakImage", "plotChromPeaks" ] }, { "page": "plotEIC-methods", "title": "Plot extracted ion chromatograms for specified m/z range", "topics": [ "plotEIC", "plotEIC,xcmsRaw-method" ] }, { "page": "plotFeatureGroups", "title": "Plot feature groups in the m/z-retention time space", "topics": [ "plotFeatureGroups" ] }, { "page": "plotMsData", "title": "DEPRECATED: Create a plot that combines a XIC and a mz/rt 2D plot for one sample", "topics": [ "plotMsData" ] }, { "page": "plotPeaks-methods", "title": "Plot a grid of a large number of peaks", "topics": [ "plotPeaks", "plotPeaks,xcmsRaw-method" ] }, { "page": "plotPrecursorIons", "title": "General visualization of precursor ions of LC-MS/MS data", "topics": [ "plotPrecursorIons" ] }, { "page": "plotQC", "title": "Plot m/z and RT deviations for QC purposes without external reference data", "topics": [ "plotQC" ] }, { "page": "plotRaw-methods", "title": "Scatterplot of raw data points", "topics": [ "plotRaw", "plotRaw,xcmsRaw-method" ] }, { "page": "plotrt-methods", "title": "Plot retention time deviation profiles", "topics": [ "plotrt", "plotrt,xcmsSet-method" ] }, { "page": "plotScan-methods", "title": "Plot a single mass scan", "topics": [ "plotScan", "plotScan,xcmsRaw-method" ] }, { "page": "plotSpec-methods", "title": "Plot mass spectra from the profile matrix", "topics": [ "plotSpec", "plotSpec,xcmsRaw-method" ] }, { "page": "plotSurf-methods", "title": "Plot profile matrix 3D surface using OpenGL", "topics": [ "plotSurf", "plotSurf,xcmsRaw-method" ] }, { "page": "plotTIC-methods", "title": "Plot total ion count", "topics": [ "plotTIC", "plotTIC,xcmsRaw-method" ] }, { "page": "ProcessHistory-class", "title": "Tracking data processing", "topics": [ "fileIndex", "fileIndex,ProcessHistory-method", "msLevel,XProcessHistory-method", "processDate", "processDate,ProcessHistory-method", "ProcessHistory", "ProcessHistory-class", "processInfo", "processInfo,ProcessHistory-method", "processParam", "processParam,XProcessHistory-method", "processType", "processType,ProcessHistory-method", "XProcessHistory", "XProcessHistory-class" ] }, { "page": "profMat-xcmsSet", "title": "The profile matrix", "topics": [ "profile-matrix", "profMat", "profMat,MsExperiment-method", "profMat,xcmsRaw-method", "profMat-xcmsSet" ] }, { "page": "profMedFilt-methods", "title": "Median filtering of the profile matrix", "topics": [ "profMedFilt", "profMedFilt,xcmsRaw-method" ] }, { "page": "profMethod-methods", "title": "Get and set method for generating profile data", "topics": [ "profMethod", "profMethod,xcmsRaw-method", "profMethod<-", "profMethod<-,xcmsRaw-method" ] }, { "page": "profRange-methods", "title": "Specify a subset of profile mode data", "topics": [ "profRange", "profRange,xcmsRaw-method" ] }, { "page": "profStep-methods", "title": "Get and set m/z step for generating profile data", "topics": [ "profStep", "profStep,xcmsRaw-method", "profStep<-", "profStep<-,xcmsRaw-method" ] }, { "page": "XCMSnExp-peak-grouping-results", "title": "Accessing mz-rt feature data values", "topics": [ "featureValues", "featureValues,XCMSnExp-method", "quantify,XCMSnExp-method" ] }, { "page": "rawEIC-methods", "title": "Get extracted ion chromatograms for specified m/z range", "topics": [ "rawEIC", "rawEIC,xcmsRaw-method" ] }, { "page": "rawMat-methods", "title": "Get a raw data matrix", "topics": [ "rawMat", "rawMat,xcmsRaw-method", "rawMat-methods" ] }, { "page": "reconstructChromPeakSpectra", "title": "Data independent acquisition (DIA): reconstruct MS2 spectra", "topics": [ "reconstructChromPeakSpectra", "reconstructChromPeakSpectra,XcmsExperiment-method", "reconstructChromPeakSpectra,XCMSnExp-method" ] }, { "page": "refineChromPeaks", "title": "Refine Identified Chromatographic Peaks", "concept": [ "chromatographic peak refinement methods" ], "topics": [ "CleanPeaksParam", "FilterIntensityParam", "MergeNeighboringPeaksParam", "refineChromPeaks", "refineChromPeaks,XcmsExperiment,CleanPeaksParam-method", "refineChromPeaks,XcmsExperiment,FilterIntensityParam-method", "refineChromPeaks,XcmsExperiment,MergeNeighboringPeaksParam-method", "refineChromPeaks,XcmsExperimentHdf5,FilterIntensityParam-method", "refineChromPeaks,XCMSnExp,CleanPeaksParam-method", "refineChromPeaks,XCMSnExp,FilterIntensityParam-method", "refineChromPeaks,XCMSnExp,MergeNeighboringPeaksParam-method" ] }, { "page": "removeIntensity-Chromatogram", "title": "Remove intensities from chromatographic data", "topics": [ "removeIntensity", "removeIntensity,Chromatogram-method", "removeIntensity,MChromatograms-method", "removeIntensity,XChromatogram-method" ] }, { "page": "retcor-methods", "title": "Correct retention time from different samples", "topics": [ "retcor", "retcor,xcmsSet-method", "retcor-methods" ] }, { "page": "retcor.obiwarp-methods", "title": "Align retention times across samples with Obiwarp", "topics": [ "retcor.obiwarp", "retcor.obiwarp,xcmsSet-method" ] }, { "page": "retcor.peakgroups-methods", "title": "Align retention times across samples", "topics": [ "retcor.linear", "retcor.linear,xcmsSet-method", "retcor.loess", "retcor.loess,xcmsSet-method", "retcor.peakgroups", "retcor.peakgroups,xcmsSet-method" ] }, { "page": "retexp", "title": "Set retention time window to a specified width", "topics": [ "retexp" ] }, { "page": "rla", "title": "Calculate relative log abundances", "topics": [ "rla", "rowRla" ] }, { "page": "RsdFilter", "title": "Filter features based on their coefficient of variation", "concept": [ "Filter features in xcms" ], "topics": [ "filterFeatures,SummarizedExperiment,RsdFilter-method", "filterFeatures,XcmsResult,RsdFilter-method", "RsdFilter" ] }, { "page": "sampnames-methods", "title": "Get sample names", "topics": [ "sampnames", "sampnames,xcmsEIC-method", "sampnames,xcmsSet-method" ] }, { "page": "showError-xcmsSet-method", "title": "Extract processing errors", "topics": [ "showError", "showError,xcmsSet-method" ] }, { "page": "specDist-methods", "title": "Distance methods for xcmsSet, xcmsRaw and xsAnnotate", "topics": [ "specDist", "specDist,xcmsSet-method", "specDist-methods" ] }, { "page": "specDist.cosine-methods", "title": "a Distance function based on matching peaks", "topics": [ "specDist.cosine", "specDist.cosine,matrix,matrix-method" ] }, { "page": "specDist.meanMZmatch-methods", "title": "a Distance function based on matching peaks", "topics": [ "specDist.meanMZmatch", "specDist.meanMZmatch,matrix,matrix-method" ] }, { "page": "specDist.peakCount-methods", "title": "a Distance function based on matching peaks", "topics": [ "specDist.peakCount", "specDist.peakCount,matrix,matrix-method", "specDist.peakCount-methods" ] }, { "page": "specNoise", "title": "Calculate noise for a sparse continuum mass spectrum", "topics": [ "specNoise" ] }, { "page": "specPeaks", "title": "Identify peaks in a sparse continuum mode spectrum", "topics": [ "specPeaks" ] }, { "page": "split.xcmsRaw", "title": "Divide an xcmsRaw object", "topics": [ "split.xcmsRaw" ] }, { "page": "split.xcmsSet", "title": "Divide an xcmsSet object", "topics": [ "split, split-methods", "split.xcmsSet" ] }, { "page": "SSgauss", "title": "Gaussian Model", "topics": [ "SSgauss" ] }, { "page": "stitch-methods", "title": "Correct gaps in data", "topics": [ "makeacqNum", "makeacqNum, xcmsRaw-method", "stitch", "stitch,xcmsRaw-method", "stitch-methods", "stitch.netCDF", "stitch.xml" ] }, { "page": "XcmsExperimentHdf5", "title": "xcms result object for very large data sets", "topics": [ "adjustRtimePeakGroups,XcmsExperimentHdf5,PeakGroupsParam-method", "chromPeakData,XcmsExperimentHdf5-method", "filterChromPeaks,XcmsExperimentHdf5-method", "filterFeatureDefinitions,XcmsExperimentHdf5-method", "toXcmsExperiment", "toXcmsExperimentHdf5", "XcmsExperimentHdf5", "XcmsExperimentHdf5-class" ] }, { "page": "updateObject-xcmsSet-method", "title": "Update an 'xcmsSet' object", "topics": [ "updateObject,xcmsSet-method" ] }, { "page": "useOriginalCode", "title": "Enable usage of old xcms code", "topics": [ "useOriginalCode" ] }, { "page": "verify.mzQuantML", "title": "Verify an mzQuantML file", "topics": [ "verify.mzQuantML" ] }, { "page": "write.cdf-methods", "title": "Save an xcmsRaw object to file", "topics": [ "write.cdf", "write.cdf,xcmsRaw-method" ] }, { "page": "write.mzdata-methods", "title": "Save an xcmsRaw object to a file", "topics": [ "write.mzdata", "write.mzdata,xcmsRaw-method" ] }, { "page": "write.mzQuantML", "title": "Save an xcmsSet object to an PSI mzQuantML file", "topics": [ "write.mzQuantML", "write.mzQuantML,xcmsSet-method" ] }, { "page": "writeMSData-XCMSnExp-character-method", "title": "Export MS data to mzML/mzXML files", "topics": [ "writeMSData,XCMSnExp,character-method" ] }, { "page": "writeMzTab", "title": "Save a grouped xcmsSet object in mzTab-1.1 format file", "topics": [ "writeMzTab" ] }, { "page": "XChromatogram", "title": "Containers for chromatographic and peak detection data", "topics": [ "chromPeakData,XChromatogram-method", "chromPeakData,XChromatograms-method", "chromPeakData<-,XChromatogram-method", "chromPeaks,XChromatogram-method", "chromPeaks,XChromatograms-method", "chromPeaks<-,XChromatogram-method", "coerce,MChromatograms,XChromatograms-method", "dropFeatureDefinitions,XChromatograms-method", "dropFilledChromPeaks,XChromatogram-method", "dropFilledChromPeaks,XChromatograms-method", "featureDefinitions,XChromatograms-method", "featureValues,XChromatograms-method", "filterChromPeaks,XChromatogram-method", "filterChromPeaks,XChromatograms-method", "filterMz,XChromatogram-method", "filterMz,XChromatograms-method", "filterRt,XChromatogram-method", "filterRt,XChromatograms-method", "groupChromPeaks,XChromatograms,PeakDensityParam-method", "hasChromPeaks,XChromatogram-method", "hasChromPeaks,XChromatograms-method", "hasFeatures,XChromatograms-method", "hasFilledChromPeaks,XChromatograms-method", "plot,XChromatogram,ANY-method", "plot,XChromatograms,ANY-method", "plotChromPeakDensity,XChromatograms-method", "processHistory,XChromatograms-method", "refineChromPeaks,XChromatogram,MergeNeighboringPeaksParam-method", "refineChromPeaks,XChromatograms,MergeNeighboringPeaksParam-method", "transformIntensity,XChromatogram-method", "transformIntensity,XChromatograms-method", "XChromatogram", "XChromatogram-class", "XChromatograms", "XChromatograms-class", "[,XChromatograms,ANY,ANY,ANY-method" ] }, { "page": "xcms-deprecated", "title": "Deprecated functions in package 'xcms'", "topics": [ "xcms-deprecated" ] }, { "page": "xcmsEIC-class", "title": "Class xcmsEIC, a class for multi-sample extracted ion chromatograms", "topics": [ "mzrange", "mzrange,xcmsEIC-method", "rtrange", "rtrange,xcmsEIC-method", "xcmsEIC-class" ] }, { "page": "xcmsFileSource-class", "title": "Base class for loading raw data from a file", "topics": [ "xcmsFileSource-class", "xcmsSource,character-method" ] }, { "page": "xcmsFragments", "title": "Constructor for xcmsFragments objects which holds Tandem MS peaks", "topics": [ "xcmsFragments" ] }, { "page": "xcmsFragments-class", "title": "Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data", "topics": [ "plotTree", "plotTree,xcmsFragments-method", "xcmsFragments-class" ] }, { "page": "XCMSnExp-class", "title": "Data container storing xcms preprocessing results", "topics": [ "adjustedRtime", "adjustedRtime,XCMSnExp-method", "adjustedRtime<-", "adjustedRtime<-,XCMSnExp-method", "c.XCMSnExp", "chromPeakData", "chromPeakData,XCMSnExp-method", "chromPeakData<-", "chromPeakData<-,XCMSnExp-method", "chromPeaks", "chromPeaks,XCMSnExp-method", "chromPeaks<-", "chromPeaks<-,XCMSnExp-method", "dropAdjustedRtime", "dropAdjustedRtime,XCMSnExp-method", "dropChromPeaks", "dropChromPeaks,XCMSnExp-method", "dropFeatureDefinitions", "dropFeatureDefinitions,XCMSnExp-method", "dropFilledChromPeaks", "dropFilledChromPeaks,XCMSnExp-method", "featureDefinitions", "featureDefinitions,XCMSnExp-method", "featureDefinitions<-", "featureDefinitions<-,XCMSnExp-method", "findChromPeaks,XCMSnExp,Param-method", "hasAdjustedRtime", "hasAdjustedRtime,XCMSnExp-method", "hasChromPeaks", "hasChromPeaks,XCMSnExp-method", "hasFeatures", "hasFeatures,XCMSnExp-method", "hasFilledChromPeaks", "hasFilledChromPeaks,XCMSnExp-method", "intensity,XCMSnExp-method", "mz,XCMSnExp-method", "plot,XCMSnExp,missing-method", "processHistory", "processHistory,XCMSnExp-method", "processHistoryTypes", "profMat,OnDiskMSnExp-method", "profMat,XCMSnExp-method", "rtime,XCMSnExp-method", "setAs", "spectra,XCMSnExp-method", "spectrapply,XCMSnExp-method", "updateObject,XCMSnExp-method", "XCMSnExp", "XCMSnExp-class" ] }, { "page": "xcmsPeaks-class", "title": "A matrix of peaks", "topics": [ "xcmsPeaks-class" ] }, { "page": "xcmsRaw", "title": "Constructor for xcmsRaw objects which reads NetCDF/mzXML files", "topics": [ "deepCopy", "deepCopy,xcmsRaw-method", "xcmsRaw" ] }, { "page": "xcmsRaw-class", "title": "Class xcmsRaw, a class for handling raw data", "topics": [ "findmzROI", "findmzROI,xcmsRaw-method", "levelplot", "mslevel,xcmsRaw-method", "profinfo,xcmsRaw-method", "profMz", "profMz,xcmsRaw-method", "revMz", "revMz,xcmsRaw-method", "scanrange,xcmsRaw-method", "sortMz", "sortMz,xcmsRaw-method", "xcmsRaw-class" ] }, { "page": "xcmsSet", "title": "Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files", "topics": [ "xcmsSet" ] }, { "page": "xcmsSet-class", "title": "Class xcmsSet, a class for preprocessing peak data", "topics": [ "$,xcmsSet-method", "$<-,xcmsSet-method", "filepaths", "filepaths,xcmsSet-method", "filepaths<-", "filepaths<-,xcmsSet-method", "groupidx", "groupidx,xcmsSet-method", "groupidx<-", "groupidx<-,xcmsSet-method", "groups", "groups,xcmsSet-method", "groups<-", "groups<-,xcmsSet-method", "mslevel", "mslevel,xcmsSet-method", "peaks", "peaks,xcmsSet-method", "peaks<-", "peaks<-,xcmsSet-method", "phenoData", "phenoData,xcmsSet-method", "phenoData<-", "phenoData<-,xcmsSet,ANY-method", "phenoData<-,xcmsSet-method", "profinfo", "profinfo,xcmsSet-method", "profinfo<-", "profinfo<-,xcmsSet-method", "profMethod,xcmsSet-method", 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