SSgauss                 Gaussian Model
c.xcmsSet               Combine xcmsSet objects
diffreport              Create report of analyte differences
etg                     Empirically Transformed Gaussian function
fillPeaks               Integrate areas of missing peaks
findMZBoxes             Find areas of high peak density in LC/MS Data
findPeaks-methods       Feature detection for GC/MS and LC/MS Data -
                        methods
findPeaks.centWave      Feature detection for centroided LC/MS data
findPeaks.matchedFilter
                        Feature detection in the chromatographic time
                        domain
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                   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           Plot log intensity image of a xcmsRaw object
medianFilter            Apply a median filter to a matrix
plot.xcmsEIC            Plot extracted ion chromatograms from multiple
                        files
plotChrom               Plot extracted ion chromatograms from the
                        profile matrix
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             Apply a median filter to 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
retcor                  Align retention times across samples
retexp                  Set retention time window to a specified width
sampnames               Get sample names
specNoise               Calculate noise for a sparse continuum mass
                        spectrum
specPeaks               Identify peaks in a sparse continuum mode
                        spectrum
split.xcmsSet           Divide an xcmsSet object
xcmsEIC-class           Class xcmsEIC, a class for multi-sample
                        extracted ion chromatograms
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
