Package index • xcms

All functions

AutoLockMass AutoLockMass-methods AutoLockMass,xcmsRaw-method: Automatic parameter for Lock mass fixing AutoLockMass ~~

BlankFlag() filterFeatures(<XcmsResult>,<BlankFlag>) filterFeatures(<SummarizedExperiment>,<BlankFlag>): Flag features based on the intensity in blank samples

DratioFilter() filterFeatures(<XcmsResult>,<DratioFilter>) filterFeatures(<SummarizedExperiment>,<DratioFilter>): Filter features based on the dispersion ratio

GenericParam(): Generic parameter class

adjustRtime(<XcmsExperiment>,<LamaParama>) matchLamasChromPeaks() summarizeLamaMatch() matchedRtimes() LamaParama() plot(<LamaParama>,<ANY>): Landmark-based alignment: aligning a dataset against an external reference

PercentMissingFilter() filterFeatures(<XcmsResult>,<PercentMissingFilter>) filterFeatures(<SummarizedExperiment>,<PercentMissingFilter>): Filter features based on the percentage of missing data

processParam(<XProcessHistory>) msLevel(<XProcessHistory>) processType(<ProcessHistory>) processDate(<ProcessHistory>) processInfo(<ProcessHistory>) fileIndex(<ProcessHistory>): Tracking data processing

RsdFilter() filterFeatures(<XcmsResult>,<RsdFilter>) filterFeatures(<SummarizedExperiment>,<RsdFilter>): Filter features based on their coefficient of variation

SSgauss(): Gaussian Model

processHistoryTypes() hasFilledChromPeaks(<XCMSnExp>) profMat(<OnDiskMSnExp>) hasAdjustedRtime(<XCMSnExp>) hasFeatures(<XCMSnExp>) hasChromPeaks(<XCMSnExp>) adjustedRtime(<XCMSnExp>) `adjustedRtime<-`(<XCMSnExp>) featureDefinitions(<XCMSnExp>) `featureDefinitions<-`(<XCMSnExp>) chromPeaks(<XCMSnExp>) `chromPeaks<-`(<XCMSnExp>) rtime(<XCMSnExp>) mz(<XCMSnExp>) intensity(<XCMSnExp>) spectra(<XCMSnExp>) processHistory(<XCMSnExp>) dropChromPeaks(<XCMSnExp>) dropFeatureDefinitions(<XCMSnExp>) dropAdjustedRtime(<XCMSnExp>) profMat(<XCMSnExp>) findChromPeaks(<XCMSnExp>,<Param>) dropFilledChromPeaks(<XCMSnExp>) spectrapply(<XCMSnExp>) c(<XCMSnExp>) chromPeakData(<XCMSnExp>) `chromPeakData<-`(<XCMSnExp>) plot(<XCMSnExp>,<missing>): Data container storing xcms preprocessing results

`[`(<XCMSnExp>,<ANY>,<ANY>,<ANY>) `[[`(<XCMSnExp>,<ANY>,<ANY>) filterMsLevel(<XCMSnExp>) filterFile(<XCMSnExp>) filterMz(<XCMSnExp>) filterRt(<XCMSnExp>) split(<XCMSnExp>,<ANY>) filterChromPeaks(<XCMSnExp>) filterFeatureDefinitions(<XCMSnExp>): XCMSnExp filtering and subsetting

bin(<XCMSnExp>) clean(<XCMSnExp>) filterAcquisitionNum(<XCMSnExp>) normalize(<XCMSnExp>) pickPeaks(<XCMSnExp>) removePeaks(<XCMSnExp>) smooth(<XCMSnExp>): XCMSnExp data manipulation methods inherited from MSnbase

quantify(<XCMSnExp>) featureValues(<XCMSnExp>): Accessing mz-rt feature data values

XChromatograms() XChromatogram() chromPeaks(<XChromatogram>) `chromPeaks<-`(<XChromatogram>) plot(<XChromatogram>,<ANY>) filterMz(<XChromatogram>) filterRt(<XChromatogram>) hasChromPeaks(<XChromatogram>) dropFilledChromPeaks(<XChromatogram>) chromPeakData(<XChromatogram>) `chromPeakData<-`(<XChromatogram>) refineChromPeaks(<XChromatogram>,<MergeNeighboringPeaksParam>) filterChromPeaks(<XChromatogram>) transformIntensity(<XChromatogram>) hasChromPeaks(<XChromatograms>) hasFilledChromPeaks(<XChromatograms>) chromPeaks(<XChromatograms>) chromPeakData(<XChromatograms>) filterMz(<XChromatograms>) filterRt(<XChromatograms>) plot(<XChromatograms>,<ANY>) processHistory(<XChromatograms>) hasFeatures(<XChromatograms>) dropFeatureDefinitions(<XChromatograms>) groupChromPeaks(<XChromatograms>,<PeakDensityParam>) featureDefinitions(<XChromatograms>) `[`(<XChromatograms>,<ANY>,<ANY>,<ANY>) featureValues(<XChromatograms>) plotChromPeakDensity(<XChromatograms>) dropFilledChromPeaks(<XChromatograms>) refineChromPeaks(<XChromatograms>,<MergeNeighboringPeaksParam>) filterChromPeaks(<XChromatograms>) transformIntensity(<XChromatograms>): Containers for chromatographic and peak detection data

filterFeatureDefinitions() filterRt(<MsExperiment>) filterMzRange(<MsExperiment>) filterMz(<MsExperiment>) filterMsLevel(<MsExperiment>) uniqueMsLevels(<MsExperiment>) filterFile(<MsExperiment>) rtime(<MsExperiment>) fromFile(<MsExperiment>) fileNames(<MsExperiment>) polarity(<MsExperiment>) filterIsolationWindow(<MsExperiment>) chromatogram(<MsExperiment>) plot(<MsExperiment>,<missing>) c(<XcmsExperiment>) `[`(<XcmsExperiment>,<ANY>,<ANY>,<ANY>) filterIsolationWindow(<XcmsExperiment>) filterRt(<XcmsExperiment>) filterMzRange(<XcmsExperiment>) filterMsLevel(<XcmsExperiment>) hasChromPeaks(<XcmsExperiment>) dropChromPeaks(<XcmsExperiment>) `chromPeaks<-`(<XcmsExperiment>) chromPeaks(<XcmsExperiment>) `chromPeakData<-`(<XcmsExperiment>) chromPeakData(<XcmsExperiment>) filterChromPeaks(<XcmsExperiment>) dropAdjustedRtime(<XcmsExperiment>) hasAdjustedRtime(<MsExperiment>) rtime(<XcmsExperiment>) adjustedRtime(<XcmsExperiment>) hasFeatures(<XcmsExperiment>) featureArea(<XcmsResult>) `featureDefinitions<-`(<XcmsExperiment>) featureDefinitions(<XcmsExperiment>) dropFeatureDefinitions(<XcmsExperiment>) hasFilledChromPeaks(<XcmsExperiment>) dropFilledChromPeaks(<XcmsExperiment>) quantify(<XcmsExperiment>) featureValues(<XcmsExperiment>) chromatogram(<XcmsExperiment>) processHistory(<XcmsExperiment>) filterFile(<XcmsExperiment>): Next Generation xcms Result Object

toXcmsExperimentHdf5() toXcmsExperiment() chromPeakData(<XcmsExperimentHdf5>) filterChromPeaks(<XcmsExperimentHdf5>) adjustRtimePeakGroups(<XcmsExperimentHdf5>,<PeakGroupsParam>) filterFeatureDefinitions(<XcmsExperimentHdf5>): xcms result object for very large data sets

absent absent,xcmsSet-method present present,xcmsSet-method: Determine which peaks are absent / present in a sample class

adjustRtime() adjustRtimePeakGroups() PeakGroupsParam() ObiwarpParam() `binSize<-`(<ObiwarpParam>): Alignment: Retention time correction methods.

applyAdjustedRtime(): Replace raw with adjusted retention times

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

c.xcmsSet c, c-methods: Combine xcmsSet objects

CalibrantMassParam() isCalibrated() calibrate(<XCMSnExp>): Calibrant mass based calibration of chromatgraphic peaks

calibrate calibrate,xcmsSet-method: Calibrate peaks for correcting unprecise m/z values

chromPeakChromatograms(): Extract an ion chromatogram for each chromatographic peak

chromPeakSpectra(): Extract spectra associated with chromatographic peaks

chromPeakSummary() BetaDistributionParam(): Chromatographic peak summaries

chromatogram(<XCMSnExp>): Extracting chromatograms

collect-methods collect collect,xcmsRaw-method collect,xcmsFragments-method: Collect MS^n peaks into xcmsFragments

correlate(<Chromatogram>,<Chromatogram>) correlate(<MChromatograms>,<missing>) correlate(<MChromatograms>,<MChromatograms>): Correlate chromatograms

diffreport diffreport,xcmsSet-method: Create report of analyte differences

dirname(<OnDiskMSnExp>) `dirname<-`(<OnDiskMSnExp>): Change the file path of an OnDiskMSnExp object

do_adjustRtime_peakGroups(): Align spectrum retention times across samples using peak groups found in most samples

do_findChromPeaks_centWave(): Core API function for centWave peak detection

do_findChromPeaks_centWaveWithPredIsoROIs() do_findChromPeaks_addPredIsoROIs(): 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

estimatePrecursorIntensity(<MsExperiment>) estimatePrecursorIntensity(<OnDiskMSnExp>): Estimate precursor intensity for MS level 2 spectra

etg(): Empirically Transformed Gaussian function

exportMetaboAnalyst(): Export data for use in MetaboAnalyst

extractMsData(<OnDiskMSnExp>) extractMsData(<XCMSnExp>): DEPRECATED: Extract a data.frame containing MS data

featureGroups(<XcmsResult>) `featureGroups<-`(<XcmsResult>): Compounding of LC-MS features

featureChromatograms(): Extract ion chromatograms for each feature

featureSpectra(): Extract spectra associated with features

featureSummary(): Simple feature summaries

fillChromPeaks() FillChromPeaksParam() ChromPeakAreaParam(): Gap Filling

fillPeaks fillPeaks,xcmsSet-method: Integrate areas of missing peaks

fillPeaks.MSW fillPeaks.MSW,xcmsSet-method: Integrate areas of missing peaks in FTICR-MS data

fillPeaks.chrom fillPeaks.chrom,xcmsSet-method: Integrate areas of missing peaks

filterColumnsIntensityAbove(<MChromatograms>) filterColumnsKeepTop(<MChromatograms>) filterColumnsIntensityAbove(<XChromatograms>) filterColumnsKeepTop(<XChromatograms>): Filtering sets of chromatographic data

filterFeatures: Filtering of features based on conventional quality assessment

findChromPeaks(<Chromatogram>,<CentWaveParam>) findChromPeaks(<MChromatograms>,<CentWaveParam>) findChromPeaks(<MChromatograms>,<MatchedFilterParam>): centWave-based peak detection in purely chromatographic data

findChromPeaks(<Chromatogram>,<MatchedFilterParam>): matchedFilter-based peak detection in purely chromatographic data

CentWaveParam() findChromPeaks(<OnDiskMSnExp>,<CentWaveParam>) as.list(<CentWaveParam>): Chromatographic peak detection using the centWave method

CentWavePredIsoParam() findChromPeaks(<OnDiskMSnExp>,<CentWavePredIsoParam>): Two-step centWave peak detection considering also isotopes

MassifquantParam() findChromPeaks(<OnDiskMSnExp>,<MassifquantParam>): Chromatographic peak detection using the massifquant method

MatchedFilterParam() findChromPeaks(<OnDiskMSnExp>,<MatchedFilterParam>): Peak detection in the chromatographic time domain

findChromPeaks(): Chromatographic Peak Detection

findChromPeaksIsolationWindow(): Data independent acquisition (DIA): peak detection in isolation windows

findMZ(): Find fragment ions in xcmsFragment objects

MSWParam() findChromPeaks(<OnDiskMSnExp>,<MSWParam>): Single-spectrum non-chromatography MS data peak detection

findPeaks-methods findPeaks findPeaks,xcmsRaw-method: Feature detection for GC/MS and LC/MS Data - methods

findPeaks.MS1 findPeaks.MS1,xcmsRaw-method: Collecting MS1 precursor peaks

findPeaks.MSW(<xcmsRaw>): Peak detection for single-spectrum non-chromatography MS data

findPeaks.addPredictedIsotopeFeatures findPeaks.addPredictedIsotopeFeatures,xcmsRaw-method: Feature detection based on predicted isotope features for high resolution LC/MS data

findPeaks.centWave findPeaks.centWave,xcmsRaw-method: Feature detection for high resolution LC/MS data

findPeaks.centWaveWithPredictedIsotopeROIs findPeaks.centWaveWithPredictedIsotopeROIs,xcmsRaw-method: Feature detection with centWave and additional isotope features

findPeaks.massifquant findPeaks.massifquant,xcmsRaw-method: Feature detection for XC-MS data.

findPeaks.matchedFilter(<xcmsRaw>): Peak detection in the chromatographic time domain

findneutral(): Find neutral losses in xcmsFragment objects

getEIC getEIC,xcmsRaw-method getEIC,xcmsSet-method: Get extracted ion chromatograms for specified m/z ranges

getPeaks getPeaks,xcmsRaw-method: Get peak intensities for specified regions

getScan getScan,xcmsRaw-method getMsnScan getMsnScan,xcmsRaw-method: Get m/z and intensity values for a single mass scan

getSpec getSpec,xcmsRaw-method: Get average m/z and intensity values for multiple mass scans

getXcmsRaw getXcmsRaw,xcmsSet-method: Load the raw data for one or more files in the xcmsSet

group-methods group group,xcmsSet-method: Group peaks from different samples together

group.density group.density,xcmsSet-method: Group peaks from different samples together

group.mzClust group.mzClust,xcmsSet-method: Group Peaks via High Resolution Alignment

group.nearest group.nearest,xcmsSet-method: Group peaks from different samples together

groupChromPeaks() PeakDensityParam() MzClustParam() NearestPeaksParam() as.list(<PeakDensityParam>): Correspondence: group chromatographic peaks across samples

groupFeatures(<XcmsResult>,<AbundanceSimilarityParam>): Compounding/feature grouping based on similarity of abundances across samples

EicSimilarityParam() groupFeatures(<XcmsResult>,<EicSimilarityParam>): Compounding/feature grouping based on similarity of extracted ion chromatograms

groupFeatures(<XcmsResult>,<SimilarRtimeParam>): Compounding/feature grouping based on similar retention times

groupOverlaps(): Group overlapping ranges

groupnames(<XCMSnExp>): Generate unique group (feature) names based on mass and retention time

groupnames groupnames,xcmsEIC-method groupnames,xcmsSet-method: Generate unque names for peak groups

groupval groupval,xcmsSet-method: Extract a matrix of peak values for each group

highlightChromPeaks(): Add definition of chromatographic peaks to an extracted chromatogram plot

image,xcmsRaw-method: Plot log intensity image of a xcmsRaw object

imputeLinInterpol(): Impute values for empty elements in a vector using linear interpolation

imputeRowMin(): Replace missing values with a proportion of the row minimum

imputeRowMinRand(): Impute missing values with random numbers based on the row minimum

isolationWindowTargetMz(<OnDiskMSnExp>): Extract isolation window target m/z definition

levelplot,xcmsRaw-method levelplot,xcmsSet-method: Plot log intensity image of a xcmsRaw object

loadRaw loadRaw-methods loadRaw,xcmsSource-method loadRaw,xcmsFileSource-method: Read binary data from a source

loadXcmsData(): LC-MS preprocessing result test data sets

manualChromPeaks() manualFeatures(): Manual peak integration and feature definition

medianFilter(): Apply a median filter to a matrix

msn2xcmsRaw(): Copy MSn data in an xcmsRaw to the MS slots

overlappingFeatures(): Identify overlapping features

peakPlots-methods peakPlots,xcmsSet-method: Plot a grid of a large number of peaks

peakTable peakTable,xcmsSet-method: Create report of aligned peak intensities

peaksWithCentWave(): Identify peaks in chromatographic data using centWave

peaksWithMatchedFilter(): Identify peaks in chromatographic data using matchedFilter

phenoDataFromPaths(): Derive experimental design from file paths

plot.xcmsEIC plot, plot-methods: Plot extracted ion chromatograms from multiple files

plotAdjustedRtime(): Visualization of Alignment Results

plotChrom plotChrom,xcmsRaw-method: Plot extracted ion chromatograms from the profile matrix

plotChromPeakDensity(<XCMSnExp>): Plot chromatographic peak density along the retention time axis

plotChromPeaks() plotChromPeakImage(): General visualizations of peak detection results

plotChromatogramsOverlay(<MChromatograms>) plotChromatogramsOverlay(<XChromatograms>): Plot multiple chromatograms into the same plot

plotEIC plotEIC,xcmsRaw-method: Plot extracted ion chromatograms for specified m/z range

plotFeatureGroups(): Plot feature groups in the m/z-retention time space

plotMsData(): DEPRECATED: Create a plot that combines a XIC and a mz/rt 2D plot for one sample

plotPeaks plotPeaks,xcmsRaw-method: Plot a grid of a large number of peaks

plotPrecursorIons(): General visualization of precursor ions of LC-MS/MS data

plotQC(): Plot m/z and RT deviations for QC purposes without external reference data

plotRaw plotRaw,xcmsRaw-method: Scatterplot of raw data points

plotScan plotScan,xcmsRaw-method: Plot a single mass scan

plotSpec plotSpec,xcmsRaw-method: Plot mass spectra from the profile matrix

plotSurf plotSurf,xcmsRaw-method: Plot profile matrix 3D surface using OpenGL

plotTIC plotTIC,xcmsRaw-method: Plot total ion count

plotrt plotrt,xcmsSet-method: Plot retention time deviation profiles

profMat(<MsExperiment>) profMat(<xcmsRaw>): The profile matrix

profMedFilt profMedFilt,xcmsRaw-method: Median filtering of the profile matrix

profMethod profMethod<- profMethod,xcmsRaw-method profMethod<-,xcmsRaw-method: Get and set method for generating profile data

profRange profRange,xcmsRaw-method: Specify a subset of profile mode data

profStep profStep<- profStep,xcmsRaw-method profStep<-,xcmsRaw-method: Get and set m/z step for generating profile data

rawEIC rawEIC,xcmsRaw-method: Get extracted ion chromatograms for specified m/z range

rawMat rawMat-methods rawMat,xcmsRaw-method: Get a raw data matrix

reconstructChromPeakSpectra(): Data independent acquisition (DIA): reconstruct MS2 spectra

refineChromPeaks() CleanPeaksParam() MergeNeighboringPeaksParam() FilterIntensityParam(): Refine Identified Chromatographic Peaks

removeIntensity(<Chromatogram>) removeIntensity(<MChromatograms>) removeIntensity(<XChromatogram>): Remove intensities from chromatographic data

retcor-methods retcor retcor,xcmsSet-method: Correct retention time from different samples

retcor.obiwarp retcor.obiwarp,xcmsSet-method: Align retention times across samples with Obiwarp

retcor.peakgroups retcor.peakgroups,xcmsSet-method retcor.loess retcor.loess,xcmsSet-method retcor.linear retcor.linear,xcmsSet-method: Align retention times across samples

retexp(): Set retention time window to a specified width

rla() rowRla(): Calculate relative log abundances

sampnames sampnames,xcmsEIC-method sampnames,xcmsSet-method: Get sample names

showError(<xcmsSet>): Extract processing errors

specDist-methods specDist specDist,xcmsSet-method: Distance methods for xcmsSet, xcmsRaw and xsAnnotate

specDist.cosine(): a Distance function based on matching peaks

specDist.meanMZmatch(): a Distance function based on matching peaks

specDist.peakCount(): 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

split.xcmsRaw: Divide an xcmsRaw object

split.xcmsSet split, split-methods: Divide an xcmsSet object

stitch stitch-methods stitch,xcmsRaw-method stitch.netCDF stitch.xml makeacqNum makeacqNum, xcmsRaw-method: Correct gaps in data

`[`(<xcmsRaw>,<logicalOrNumeric>,<missing>,<missing>): Subset an xcmsRaw object by scans

updateObject(<xcmsSet>): Update an xcmsSet object

useOriginalCode(): Enable usage of old xcms code

verify.mzQuantML(): Verify an mzQuantML file

write.cdf write.cdf,xcmsRaw-method: Save an xcmsRaw object to file

write.mzQuantML write.mzQuantML,xcmsSet-method: Save an xcmsSet object to an PSI mzQuantML file

write.mzdata write.mzdata,xcmsRaw-method: Save an xcmsRaw object to a file

writeMSData(<XCMSnExp>,<character>): Export MS data to mzML/mzXML files

writeMzTab: Save a grouped xcmsSet object in mzTab-1.1 format file

xcms-deprecated: Deprecated functions in package ‘xcms’

xcmsEIC-class mzrange,xcmsEIC-method mzrange rtrange,xcmsEIC-method rtrange: Class xcmsEIC, a class for multi-sample extracted ion chromatograms

xcmsFileSource-class xcmsSource,character-method: Base class for loading raw data from a file

xcmsFragments-class plotTree plotTree,xcmsFragments-method: Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data

xcmsFragments(): Constructor for xcmsFragments objects which holds Tandem MS peaks

xcmsPeaks-class: A matrix of peaks

xcmsRaw-class mslevel,xcmsRaw-method profinfo,xcmsRaw-method profMz,xcmsRaw-method profMz revMz,xcmsRaw-method revMz scanrange,xcmsRaw-method sortMz,xcmsRaw-method sortMz levelplot findmzROI findmzROI,xcmsRaw-method: Class xcmsRaw, a class for handling raw data

xcmsRaw() deepCopy(): Constructor for xcmsRaw objects which reads NetCDF/mzXML files

xcmsSet-class [,xcmsSet-method [,xcmsSet,ANY,ANY,ANY-method $<-,xcmsSet-method $,xcmsSet-method filepaths<-,xcmsSet-method filepaths<- filepaths,xcmsSet-method filepaths groupidx<-,xcmsSet-method groupidx<- groupidx,xcmsSet-method groupidx groups<-,xcmsSet-method groups<- groups,xcmsSet-method groups mslevel,xcmsSet-method mslevel peaks<-,xcmsSet-method peaks<- peaks,xcmsSet-method peaks phenoData phenoData,xcmsSet-method phenoData<- phenoData<-,xcmsSet-method phenoData<-,xcmsSet,ANY-method profinfo<-,xcmsSet-method profinfo<- profinfo,xcmsSet-method profinfo profMethod,xcmsSet-method profStep,xcmsSet-method progressCallback progressCallback,xcmsSet-method progressCallback<- progressCallback<-,xcmsSet-method sampclass<-,xcmsSet-method sampclass<- sampclass,xcmsSet-method sampclass sampnames<-,xcmsSet-method sampnames<- scanrange,xcmsSet-method scanrange: Class xcmsSet, a class for preprocessing peak data

xcmsSet(): Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files

xcmsSource-class: Virtual class for raw data sources

xcmsSource xcmsSource-methods xcmsSource,xcmsSource-method: Create an xcmsSource object in a flexible way