# Clustering of MS2 Spectra for Metabolite Identification

## Documentation for package ‘CluMSID’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

accessAnnotation | Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objects
accessID | Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objects
accessNeutralLosses | Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objects
accessors | Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objects
accessPolarity | Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objects
accessPrecursor | Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objects
accessRT | Accessor functions for individual slots of 'MS2spectrum' and 'pseudospectrum' objects
accessSpectrum | 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
cossim-method | 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
HCplot | Generate cluster dendrogram or heatmap from spectral similarity data
HCtbl | Hierarchical clustering of spectral similarity data
intensity-method | A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation
MDSplot | Multidimensional scaling of spectral similarity data
mergeMS2spectra | Merge MS2 spectra with or without external peak table
MS2spectrum-class | A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation
mz-method | A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation
networkplot | Correlation network from spectral similarity data
OPTICSplot | Visualisation of density-based clustering of spectral similarity data
OPTICStbl | Density-based clustering of spectral similarity data
peaksCount-method | A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation
precursorMz-method | A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation
pseudospectrum-class | A custom S4 class for MS1 pseudospectra and respective metainformation
rtime-method | A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation
show-method | A custom S4 class for MS2 spectra, neutral loss patterns 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