AutoLockMass-methods    Automatic parameter for Lock mass fixing
                        'AutoLockMass' ~~
CalibrantMassParam-class
                        Calibrant mass based calibration of
                        chromatgraphic peaks
CleanPeaksParam         Remove chromatographic peaks with too large rt
                        width
FillChromPeaksParam-class
                        Integrate areas of missing peaks
GenericParam-class      Generic parameter class
MergeNeighboringPeaksParam
                        Merge neighboring and overlapping
                        chromatographic peaks
ProcessHistory-class    Tracking data processing
SSgauss                 Gaussian Model
XCMSnExp-class          Data container storing xcms preprocessing
                        results
XChromatograms          Containers for chromatographic and peak
                        detection data
[,xcmsRaw,logicalOrNumeric,missing,missing-method
                        Subset an xcmsRaw object by scans
absent                  Determine which peaks are absent / present in a
                        sample class
adjustRtime             Alignment: Retention time correction methods.
adjustRtime-obiwarp     Align retention times across samples using
                        Obiwarp
adjustRtime-peakGroups
                        Retention time correction based on alignment of
                        house keeping peak groups
align,Chromatogram,Chromatogram-method
                        Aligning chromatographic data
applyAdjustedRtime      Replace raw with adjusted retention times
bin,XCMSnExp-method     XCMSnExp data manipulation methods inherited
                        from MSnbase
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               Combine xcmsSet objects
calibrate               Calibrate peaks for correcting unprecise m/z
                        values
chromPeakSpectra        Extract (MS2) spectra associated with
                        chromatographic peaks
chromatogram,XCMSnExp-method
                        Extracting chromatograms
chromatographic-peak-detection
                        Chromatographic peak detection methods.
collect-methods         Collect MS^n peaks into xcmsFragments
correlate,Chromatogram,Chromatogram-method
                        Correlate chromatograms
diffreport              Create report of analyte differences
dirname                 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
                        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
etg                     Empirically Transformed Gaussian function
exportMetaboAnalyst     Export data for use in MetaboAnalyst
extractMsData,OnDiskMSnExp-method
                        DEPRECATED: Extract a 'data.frame' containing
                        MS data
featureChromatograms    Extract ion chromatograms for each feature
featureSpectra          Extract (MS2) spectra associated with features
featureSummary          Simple feature summaries
fillPeaks               Integrate areas of missing peaks
fillPeaks.MSW           Integrate areas of missing peaks in FTICR-MS
                        data
fillPeaks.chrom         Integrate areas of missing peaks
filterFeatureDefinitions
                        XCMSnExp filtering and subsetting
findChromPeaks,Chromatogram,CentWaveParam-method
                        centWave-based peak detection in purely
                        chromatographic data
findChromPeaks,Chromatogram,MatchedFilterParam-method
                        matchedFilter-based peak detection in purely
                        chromatographic data
findChromPeaks-centWave
                        Chromatographic peak detection using the
                        centWave method
findChromPeaks-centWaveWithPredIsoROIs
                        Two-step centWave peak detection considering
                        also isotopes
findChromPeaks-massifquant
                        Chromatographic peak detection using the
                        massifquant method
findChromPeaks-matchedFilter
                        Peak detection in the chromatographic time
                        domain
findChromPeaksIsolationWindow
                        Data independent acquisition (DIA): peak
                        detection in isolation windows
findMZ                  Find fragment ions in xcmsFragment objects
findPeaks-MSW           Single-spectrum non-chromatography MS data peak
                        detection
findPeaks-methods       Feature detection for GC/MS and LC/MS Data -
                        methods
findPeaks.MS1           Collecting MS1 precursor peaks
findPeaks.MSW,xcmsRaw-method
                        Peak detection for single-spectrum
                        non-chromatography MS data
findPeaks.addPredictedIsotopeFeatures
                        Feature detection based on predicted isotope
                        features for high resolution LC/MS data
findPeaks.centWave      Feature detection for high resolution LC/MS
                        data
findPeaks.centWaveWithPredictedIsotopeROIs
                        Feature detection with centWave and additional
                        isotope features
findPeaks.massifquant   Feature detection for XC-MS data.
findPeaks.matchedFilter,xcmsRaw-method
                        Peak detection in the chromatographic time
                        domain
findneutral             Find neutral losses in xcmsFragment objects
getEIC                  Get extracted ion chromatograms for specified
                        m/z ranges
getPeaks                Get peak intensities for specified regions
getScan                 Get m/z and intensity values for a single mass
                        scan
getSpec                 Get average m/z and intensity values for
                        multiple mass scans
getXcmsRaw              Load the raw data for one or more files in the
                        xcmsSet
group-methods           Group peaks from different samples together
group.density           Group peaks from different samples together
group.mzClust           Group Peaks via High Resolution Alignment
group.nearest           Group peaks from different samples together
groupChromPeaks         Correspondence: Chromatographic peak grouping
                        methods.
groupChromPeaks-density
                        Peak grouping based on time dimension peak
                        densities
groupChromPeaks-mzClust
                        High resolution peak grouping for single
                        spectra samples
groupChromPeaks-nearest
                        Peak grouping based on proximity in the mz-rt
                        space
groupOverlaps           Group overlapping ranges
groupnames              Generate unque names for peak groups
groupnames,XCMSnExp-method
                        Generate unique group (feature) names based on
                        mass and retention time
groupval                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-method
                        Extract isolation window target m/z definition
levelplot,xcmsRaw-method
                        Plot log intensity image of a xcmsRaw object
loadRaw-methods         Read binary data from a source
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       Plot a grid of a large number of peaks
peakTable               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 extracted ion chromatograms from multiple
                        files
plotAdjustedRtime       Visualization of alignment results
plotChrom               Plot extracted ion chromatograms from the
                        profile matrix
plotChromPeakDensity,XCMSnExp-method
                        Plot chromatographic peak density along the
                        retention time axis
plotChromPeaks          General visualizations of peak detection
                        results
plotEIC                 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
plotQC                  Plot m/z and RT deviations for QC purposes
                        without external reference data
plotRaw                 Scatterplot of raw data points
plotScan                Plot a single mass scan
plotSpec                Plot mass spectra from the profile matrix
plotSurf                Plot profile matrix 3D surface using OpenGL
plotTIC                 Plot total ion count
plotrt                  Plot retention time deviation profiles
profMat-xcmsSet         The profile matrix
profMedFilt             Median filtering of the profile matrix
profMethod              Get and set method for generating profile data
profRange               Specify a subset of profile mode data
profStep                Get and set m/z step for generating profile
                        data
quantify,XCMSnExp-method
                        Accessing mz-rt feature data values
rawEIC                  Get extracted ion chromatograms for specified
                        m/z range
rawMat-methods          Get a raw data matrix
reconstructChromPeakSpectra
                        Data independent acquisition (DIA): reconstruct
                        MS2 spectra
retcor-methods          Correct retention time from different samples
retcor.obiwarp          Align retention times across samples with
                        Obiwarp
retcor.peakgroups       Align retention times across samples
retexp                  Set retention time window to a specified width
rla                     Calculate relative log abundances 'rla'
                        calculates the relative log abundances (RLA,
                        see reference) on a 'numeric' vector.
sampnames               Get sample names
showError,xcmsSet-method
                        Extract processing errors
specDist-methods        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-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
split.xcmsRaw           Divide an xcmsRaw object
split.xcmsSet           Divide an xcmsSet object
stitch-methods          Correct gaps in data
updateObject,xcmsSet-method
                        Update an 'xcmsSet' object
useOriginalCode         Enable usage of old xcms code
verify.mzQuantML        Verify an mzQuantML file
write.cdf               Save an xcmsRaw object to file
write.mzQuantML         Save an xcmsSet object to an PSI mzQuantML file
write.mzdata            Save an xcmsRaw object to a file
writeMSData,XCMSnExp,character-method
                        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           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
xcmsPapply              _Deprecated_: xcmsPapply
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-class        Virtual class for raw data sources
xcmsSource-methods      Create an 'xcmsSource' object in a flexible way
