Clustering of MS2 Spectra for Metabolite Identification


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Documentation for package ‘CluMSID’ version 1.0.0

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