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| mineMS2-package | Mining of MS-MS spectra by FSM |
| annotateNetwork | Title |
| calculateCoverage-method | Calculate the coverage of all the patterns in the dataset. |
| discretizeMassFragments-method | Discretize the fragments of mass spectrometers. |
| discretizeMassLosses-method | Discretize the mass differences. |
| exportLattice-method | Export a lattice |
| filterPatterns | Title |
| find | find patterns or spectra form a set of pattern or spectra ids |
| find.patterns.class | Find biggest F1 score |
| findFormula | findFormula function |
| findGNPSComponents | Find the annotable component of a GNPS network. |
| findMz | Search in an ms2Lib object? |
| findPatternsExplainingComponents | Find pattern explainig components |
| fragPattern | fragPattern constructor |
| getExtendedSpec | Return the spectrum considered while building the graph. |
| getInfo | Return the available informationon a lost of a spectra. |
| kLatticeReduction | Reduce the lattice to k nodes. |
| lossesTable | export loss table |
| mineClosedSubgraphs-method | Mine recurrent subgraph from a set of graphs. |
| ms2Lib | A class storing a set of MS-MS spectra, their associated graphs, and some supplemnetary inofmration. |
| ms2Lib | ms2Lib constructor |
| ms2Lib-class | A class storing a set of MS-MS spectra, their associated graphs, and some supplemnetary inofmration. |
| penalizedLossesDefault | Default table of penalized loss |
| plot-method | plotting a fargPattern object. |
| plot-method | Plot an element given an idx |
| plotLattice | Plot the lattice of an ms2Lib object |
| plotOccurences-method | PLotting the occurences of a fragPattern object inside an ms2Lib object. |
| plotPatterns | Plot patterns and occurences of an ms2Lib object |
| score-method | Determine scores |
| scoreLosses-method | Determine edges scores |
| scorePatterns-method | Score the patterns contained in an ms2Lib object |
| select | Selection function |
| setComponents-method | Set the components on an ms2LibSplit object. |
| vrange-method | Return the range of iteration on an ms2Lib object. |
| [-method | Return the dag correspodning to a spectra or the modif. |