This class implements different scores for peaks found in SRM/MRM. More...
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/ALGO/MRMScoring.h>
| Public Types | |
| typedef std::map< int, double > | XCorrArrayType | 
| Type definitions.  More... | |
| typedef std::vector < std::vector< XCorrArrayType > > | XCorrMatrixType | 
| Cross Correlation matrix.  More... | |
| typedef std::string | String | 
| typedef OpenSwath::SpectrumPtr | SpectrumType | 
| typedef OpenSwath::LightTransition | TransitionType | 
| typedef OpenSwath::LightPeptide | PeptideType | 
| typedef OpenSwath::LightProtein | ProteinType | 
| typedef boost::shared_ptr < OpenSwath::IFeature > | FeatureType | 
| Public Member Functions | |
| Accessors | |
| const XCorrMatrixType & | getXCorrMatrix () const | 
| non-muteable access to the Cross-correlation matrix  More... | |
| Private Attributes | |
| Members | |
| XCorrMatrixType | xcorr_matrix_ | 
| the precomputed cross correlation matrix  More... | |
| Scores | |
| void | initializeXCorrMatrix (OpenSwath::IMRMFeature *mrmfeature, OpenSwath::ITransitionGroup *transition_group, bool normalize) | 
| Initialize the scoring object and building the cross-correlation matrix.  More... | |
| double | calcXcorrCoelutionScore () | 
| calculate the cross-correlation score  More... | |
| double | calcXcorrShape_score () | 
| calculate the cross-correlation shape score  More... | |
| double | calcXcorrShape_score_weighted (const std::vector< double > &normalized_library_intensity) | 
| calculate the weighted cross-correlation shape score  More... | |
| double | calcXcorrCoelutionScore_weighted (const std::vector< double > &normalized_library_intensity) | 
| calculate the weighted cross-correlation score  More... | |
| static void | calcLibraryScore (OpenSwath::IMRMFeature *mrmfeature, const std::vector< TransitionType > &transitions, double &correlation, double &rmsd, double &manhattan, double &dotprod) | 
| calculate the library correlation score (correlation and rmsd)  More... | |
| static double | calcRTScore (const PeptideType &peptide, double normalized_experimental_rt) | 
| calculate the retention time correlation score  More... | |
| static double | calcSNScore (OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators) | 
| calculate the Signal to Noise ratio  More... | |
This class implements different scores for peaks found in SRM/MRM.
It uses scores based on different parameters of the peaks from the individual transitions and stores them individually. The idea and the scores are based on the following paper: Reiter L, Rinner O, Picotti P, Httenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011 May;8(5):430-5. Epub 2011 Mar 20.
The currently implemented scores include:
| typedef boost::shared_ptr<OpenSwath::IFeature> FeatureType | 
| typedef OpenSwath::LightPeptide PeptideType | 
| typedef OpenSwath::LightProtein ProteinType | 
| typedef OpenSwath::SpectrumPtr SpectrumType | 
| typedef std::string String | 
| typedef std::map<int, double> XCorrArrayType | 
Type definitions.
Cross Correlation array
| typedef std::vector<std::vector<XCorrArrayType> > XCorrMatrixType | 
Cross Correlation matrix.
| 
 | static | 
calculate the library correlation score (correlation and rmsd)
| 
 | static | 
calculate the retention time correlation score
| 
 | static | 
calculate the Signal to Noise ratio
| double calcXcorrCoelutionScore | ( | ) | 
calculate the cross-correlation score
| double calcXcorrCoelutionScore_weighted | ( | const std::vector< double > & | normalized_library_intensity | ) | 
calculate the weighted cross-correlation score
| double calcXcorrShape_score | ( | ) | 
calculate the cross-correlation shape score
calculate the weighted cross-correlation shape score
| const XCorrMatrixType& getXCorrMatrix | ( | ) | const | 
non-muteable access to the Cross-correlation matrix
| void initializeXCorrMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, | 
| OpenSwath::ITransitionGroup * | transition_group, | ||
| bool | normalize | ||
| ) | 
Initialize the scoring object and building the cross-correlation matrix.
| 
 | private | 
the precomputed cross correlation matrix
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:38 using doxygen 1.8.5 |