Man pages for CluMSID
Clustering of MS2 Spectra for Metabolite Identification
| accessors | Accessor functions for individual slots of 'MS2spectrum' and... |
| 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... |
| 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... |
| HCplot | Generate cluster dendrogram or heatmap from spectral... |
| HCtbl | Hierarchical clustering of spectral similarity data |
| MDSplot | Multidimensional scaling of spectral similarity data |
| mergeMS2spectra | Merge MS2 spectra with or without external peak table |
| mergeSpecList | Merge list of spectra |
| mergeTolerance | Merge spectra with m/z tolerance |
| MS2spectrum-class | A custom S4 class for MS2 spectra, neutral loss patterns and... |
| networkplot | Correlation network from spectral similarity data |
| neutrallossPatterns | Generate neutral loss patterns from MS2 spectra |
| OPTICSplot | Visualisation of density-based clustering of spectral... |
| OPTICStbl | Density-based clustering of spectral similarity data |
| pseudospectrum-class | A custom S4 class for MS1 pseudospectra and respective... |
| 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 |
