annotate                Automatic deconvolution/annotation of LC/ESI-MS
                        data
annotateDiffreport      Automatic deconvolution/annotation of LC/ESI-MS
                        data
calcCaS                 EIC correlation grouping of LC/ESI-MS data
calcCiS                 Calculate peak distance matrix after EIC
                        correlation
calcIsotopes            Calculate isotope distance matrix from
                        xsAnnotate object
calcPC,xsAnnotate-method
                        Peakclustering into pseudospectra according to
                        a distance matrix
calcPC.hcs              Peakclustering into pseudospectra with the
                        highly connected subgraphs approach
calcPC.lpc              Peakclustering into pseudospectra with the
                        label-propagation-community algorithm
cleanParallel           Cleans up with spawned slave processes after
                        use
combinexsAnnos          Check CAMERA ion species annotation due to
                        matching with opposite ion mode
compoundLibraries       The supported compound databases
compoundQuantiles       compoundQuantiles constructor
compoundQuantiles-class
                        Class compoundQuantiles encapsulates compound
                        statistics from different databases.
findAdducts             Calculate Adducts and Annotate LC/ESI-MS
                        Spectra
findIsotopes            Deconvolute/Annotate LC/ESI-MS data
findIsotopesWithValidation
                        Deconvolute/Annotate LC/ESI-MS data
findKendrickMasses      Find specfic mass defects using Kendrick mass
                        scales
findNeutralLoss         Find pseudospectra that contains a specific
                        neutral loss
findNeutralLossSpecs    Find pseudospectra that contains a specific
                        neutral loss
getAllPeakEICs          Generate EIC information from raw data
getAtomCount,compoundQuantiles-method
                        The number of atoms of the given element
getIsotopeCluster       Retrieve the annotatad isotopes
getIsotopeProportion,compoundQuantiles-method
                        The proportion of the intensities of two
                        isotope peaks
getPeaklist             Generate the annotatad peaklist
getReducedPeaklist      Generate reduced peaklist from the annotatad
                        peaklist
getpspectra             Retrieve a peaklist of one or more
                        pseudospectra
groupCorr               EIC correlation grouping of LC/ESI-MS data
groupDen                Density-Grouping of LC/ESI-MS data
groupFWHM               FWHM-Grouping of LC/ESI-MS data
massWindowSizes         The supported mass window sizes
mm14                    Extract of marker mixture 14 LC/MS data
plotEICs.xsAnnotate     Plot extracted ion chromatograms from
                        (multiple) Pseudospectra
plotPsSpectrum.xsAnnotate
                        Plot a Pseudospectrum
psDist-methods          Distance methods for xsAnnotate
pspec2metfrag           Export the putative fragments as MetFrag query
                        files
ruleSet-class           Class 'ruleSet'
xsAnnotate              xsAnnotate constructor for an provided xcmsSet
                        object
xsAnnotate-class        Class xsAnnotate, a class for annotated peak
                        data
