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 |