HCplot                  Generate cluster dendrogram or heatmap from
                        spectral similarity data
HCtbl                   Hierarchical clustering of spectral similarity
                        data
MDSplot                 Multidimensional scaling of spectral similarity
                        data
MS2spectrum-class       A custom S4 class for MS2 spectra, neutral loss
                        patterns and respective metainformation
OPTICSplot              Visualisation of density-based clustering of
                        spectral similarity data
OPTICStbl               Density-based clustering of spectral similarity
                        data
accessors               Accessor functions for individual slots of
                        'MS2spectrum' and 'pseudospectrum' objects
addAnnotations          Adding external annotations to list of
                        'MS2spectrum' objects
as.MS2spectrum          Convert spectra from 'MSnbase' classes
cossim                  Calculate cosine similarity between two spectra
distanceMatrix          Create distance matrix from list of spectra
extractMS2spectra       Extract MS2 spectra from raw data files
extractPseudospectra    Extract pseudospectra
featureList             Generate a 'data.frame' with feature
                        information from list of 'MS2spectrum' objects
findFragment            Find spectra that contain a specific fragment
findNL                  Find spectra that contain a specific neutral
                        loss
getSimilarities         Match one spectrum against a set of spectra
getSpectrum             Access individual spectra from a list of
                        spectra by various slot entries
mergeMS2spectra         Merge MS2 spectra with or without external peak
                        table
networkplot             Correlation network from spectral similarity
                        data
pseudospectrum-class    A custom S4 class for MS1 pseudospectra and
                        respective metainformation
specplot                Create a basic plot of MS2 spectra
splitPolarities         Separate spectra with different polarities from
                        the same run
writeFeaturelist        Write feature information from list of
                        'MS2spectrum' objects
