SSgauss                 Gaussian Model
absent                  Determine which peaks are absent / present in a
                        sample class
c.xcmsSet               Combine xcmsSet objects
calibrate               Calibrate peaks for correcting unprecise m/z
                        values
collect-methods         Collect MS^n peaks into xcmsFragments
diffreport              Create report of analyte differences
etg                     Empirically Transformed Gaussian function
fillPeaks               Integrate areas of missing peaks
fillPeaks.MSW           Integrate areas of missing peaks in FTICR-MS
                        data
fillPeaks.chrom         Integrate areas of missing peaks
findMZ                  Find fragment ions in xcmsFragment objects
findPeaks-methods       Feature detection for GC/MS and LC/MS Data -
                        methods
findPeaks.MS1           Collecting MS1 precursor peaks
findPeaks.MSW           Feature detection for single-spectrum
                        non-chromatography MS data
findPeaks.centWave      Feature detection for high resolution LC/MS
                        data
findPeaks.matchedFilter
                        Feature 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
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
groupnames              Generate unque names for peak groups
groupval                Extract a matrix of peak values for each group
image,xcmsRaw-method    Plot log intensity image of a xcmsRaw object
medianFilter            Apply a median filter to a matrix
peakTable               Create report of aligned peak intensities
plot.xcmsEIC            Plot extracted ion chromatograms from multiple
                        files
plotChrom               Plot extracted ion chromatograms from the
                        profile matrix
plotEIC                 Plot extracted ion chromatograms for specified
                        m/z range
plotPeaks               Plot a grid of a large number of peaks
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
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
rawEIC                  Get extracted ion chromatograms for specified
                        m/z range
rawMat-methods          Get a raw data matrix
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
sampnames               Get sample names
score_fun               Scoring for MS/MS spectra
score_fun.cor           Scoring for MS/MS spectra Via correlation
score_fun.distMatrix    Scoring for MS/MS spectra
searchMetlin            Search Metlin Online Database
simSearch               Unrestricted precursor Metlin Search
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
write.cdf               Save an xcmsRaw object to file
write.mzdata            Save an xcmsRaw object to a file
xcmsEIC-class           Class xcmsEIC, a class for multi-sample
                        extracted ion chromatograms
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              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
