Function	Description
c.xcmsSet	Combine xcmsSet objects
diffreport	Create report of analyte differences
etg	Empirically Transformed Gaussian function
fillPeaks	Integrate areas of missing peaks
findPeaks	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	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
plotrt	Plot retention time deviation profiles
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
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
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
SSgauss	Gaussian Model
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