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 |