OpenMS
2.8.0
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This class implements different scores for peaks found in SRM/MRM. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMScoring.h>
Public Types | |
typedef OpenSwath::Scoring::XCorrArrayType | XCorrArrayType |
Type definitions. More... | |
typedef OpenMS::Matrix< XCorrArrayType > | XCorrMatrixType |
Cross Correlation matrix. More... | |
typedef OpenSwath::SpectrumPtr | SpectrumType |
typedef OpenSwath::LightTransition | TransitionType |
typedef OpenSwath::LightCompound | PeptideType |
typedef OpenSwath::LightProtein | ProteinType |
typedef boost::shared_ptr< OpenSwath::IFeature > | FeatureType |
Public Member Functions | |
Accessors | |
const XCorrMatrixType & | getXCorrMatrix () const |
non-mutable access to the cross-correlation matrix More... | |
const XCorrMatrixType & | getXCorrContrastMatrix () const |
non-mutable access to the cross-correlation contrast matrix More... | |
const XCorrMatrixType & | getXCorrPrecursorContrastMatrix () const |
non-mutable access to the cross-correlation precursor contrast matrix More... | |
const XCorrMatrixType & | getXCorrPrecursorCombinedMatrix () const |
non-mutable access to the cross-correlation precursor contrast matrix More... | |
Private Attributes | |
Members | |
XCorrMatrixType | xcorr_matrix_ |
the precomputed cross correlation matrix More... | |
OpenMS::Matrix< int > | xcorr_matrix_max_peak_ |
contains max Peaks from xcorr_matrix_ More... | |
OpenMS::Matrix< double > | xcorr_matrix_max_peak_sec_ |
XCorrMatrixType | xcorr_contrast_matrix_ |
the precomputed contrast cross correlation More... | |
OpenMS::Matrix< double > | xcorr_contrast_matrix_max_peak_sec_ |
contains max Peaks from xcorr_contrast_matrix_ More... | |
XCorrMatrixType | xcorr_precursor_matrix_ |
the precomputed cross correlation matrix of the MS1 trace More... | |
XCorrMatrixType | xcorr_precursor_contrast_matrix_ |
the precomputed cross correlation against the MS1 trace More... | |
XCorrMatrixType | xcorr_precursor_combined_matrix_ |
the precomputed cross correlation with the MS1 trace More... | |
OpenMS::Matrix< double > | mi_matrix_ |
the precomputed mutual information matrix More... | |
OpenMS::Matrix< double > | mi_contrast_matrix_ |
the precomputed contrast mutual information matrix More... | |
OpenMS::Matrix< double > | mi_precursor_matrix_ |
the precomputed mutual information matrix of the MS1 trace More... | |
OpenMS::Matrix< double > | mi_precursor_contrast_matrix_ |
the precomputed contrast mutual information matrix against the MS1 trace More... | |
OpenMS::Matrix< double > | mi_precursor_combined_matrix_ |
the precomputed contrast mutual information matrix with the MS1 trace More... | |
Scores | |
void | initializeXCorrMatrix (const std::vector< std::vector< double > > &data) |
Initialize the scoring object and building the cross-correlation matrix. More... | |
void | initializeXCorrMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids) |
Initialize the scoring object and building the cross-correlation matrix. More... | |
void | initializeXCorrContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids_set1, const std::vector< std::string > &native_ids_set2) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions) More... | |
void | initializeXCorrPrecursorMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids) |
Initialize the scoring object and building the cross-correlation matrix. More... | |
void | initializeXCorrPrecursorContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions. More... | |
void | initializeXCorrPrecursorContrastMatrix (const std::vector< std::vector< double > > &data_precursor, const std::vector< std::vector< double > > &data_fragments) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions. More... | |
void | initializeXCorrPrecursorCombinedMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes and transitions. More... | |
double | calcXcorrCoelutionScore () |
Calculate the cross-correlation coelution score. More... | |
double | calcXcorrCoelutionWeightedScore (const std::vector< double > &normalized_library_intensity) |
Calculate the weighted cross-correlation coelution score. More... | |
double | calcXcorrContrastCoelutionScore () |
calculate the cross-correlation contrast score More... | |
std::vector< double > | calcSeparateXcorrContrastCoelutionScore () |
calculate the separate cross-correlation contrast score More... | |
double | calcXcorrPrecursorCoelutionScore () |
calculate the precursor cross-correlation contrast score More... | |
double | calcXcorrPrecursorContrastCoelutionScore () |
Calculate the precursor cross-correlation contrast score against the transitions. More... | |
double | calcXcorrPrecursorCombinedCoelutionScore () |
calculate the precursor cross-correlation coelution score including the transitions More... | |
double | calcXcorrShapeScore () |
Calculate the cross-correlation shape score. More... | |
double | calcXcorrShapeWeightedScore (const std::vector< double > &normalized_library_intensity) |
Calculate the weighted cross-correlation shape score. More... | |
double | calcXcorrContrastShapeScore () |
calculate the cross-correlation contrast shape score More... | |
std::vector< double > | calcSeparateXcorrContrastShapeScore () |
calculate the separate cross-correlation contrast shape score More... | |
double | calcXcorrPrecursorShapeScore () |
calculate the precursor cross-correlation shape score More... | |
double | calcXcorrPrecursorContrastShapeScore () |
calculate the precursor cross-correlation shape score against the transitions More... | |
double | calcXcorrPrecursorCombinedShapeScore () |
calculate the precursor cross-correlation shape score including the transitions More... | |
const OpenMS::Matrix< double > & | getMIMatrix () const |
non-mutable access to the MI matrix More... | |
const OpenMS::Matrix< double > & | getMIContrastMatrix () const |
non-mutable access to the MI contrast matrix More... | |
const OpenMS::Matrix< double > & | getMIPrecursorContrastMatrix () const |
non-mutable access to the MI precursor contrast matrix More... | |
const OpenMS::Matrix< double > & | getMIPrecursorCombinedMatrix () const |
non-mutable access to the MI precursor combined matrix More... | |
void | initializeMIMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids) |
Initialize the scoring object and building the MI matrix. More... | |
void | initializeMIContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids_set1, const std::vector< std::string > &native_ids_set2) |
Initialize the scoring object and building the MI matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions) More... | |
void | initializeMIPrecursorMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids) |
Initialize the scoring object and building the MI matrix. More... | |
void | initializeMIPrecursorContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids) |
Initialize the mutual information vector against the MS1 trace. More... | |
void | initializeMIPrecursorCombinedMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids) |
Initialize the mutual information vector with the MS1 trace. More... | |
double | calcMIScore () |
double | calcMIWeightedScore (const std::vector< double > &normalized_library_intensity) |
double | calcMIPrecursorScore () |
double | calcMIPrecursorContrastScore () |
double | calcMIPrecursorCombinedScore () |
std::vector< double > | calcSeparateMIContrastScore () |
static void | calcLibraryScore (OpenSwath::IMRMFeature *mrmfeature, const std::vector< TransitionType > &transitions, double &correlation, double &norm_manhattan, double &manhattan, double &dotprod, double &spectral_angle, double &rmsd) |
calculate the library correlation score 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... | |
static std::vector< double > | calcSeparateSNScore (OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators) |
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, Huettenhain 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::LightCompound PeptideType |
typedef OpenSwath::LightProtein ProteinType |
typedef OpenSwath::SpectrumPtr SpectrumType |
Type definitions.
Cross Correlation array
typedef OpenMS::Matrix<XCorrArrayType> XCorrMatrixType |
Cross Correlation matrix.
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calculate the library correlation score
double calcMIPrecursorCombinedScore | ( | ) |
double calcMIPrecursorContrastScore | ( | ) |
double calcMIPrecursorScore | ( | ) |
double calcMIScore | ( | ) |
double calcMIWeightedScore | ( | const std::vector< double > & | normalized_library_intensity | ) |
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calculate the retention time correlation score
std::vector<double> calcSeparateMIContrastScore | ( | ) |
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std::vector<double> calcSeparateXcorrContrastCoelutionScore | ( | ) |
calculate the separate cross-correlation contrast score
std::vector<double> calcSeparateXcorrContrastShapeScore | ( | ) |
calculate the separate cross-correlation contrast shape score
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static |
calculate the Signal to Noise ratio
double calcXcorrCoelutionScore | ( | ) |
Calculate the cross-correlation coelution score.
The score is a distance where zero indicates perfect coelution.
double calcXcorrCoelutionWeightedScore | ( | const std::vector< double > & | normalized_library_intensity | ) |
Calculate the weighted cross-correlation coelution score.
The score is a distance where zero indicates perfect coelution. The score is weighted by the transition intensities, non-perfect coelution in low-intensity transitions should thus become less important.
double calcXcorrContrastCoelutionScore | ( | ) |
calculate the cross-correlation contrast score
double calcXcorrContrastShapeScore | ( | ) |
calculate the cross-correlation contrast shape score
double calcXcorrPrecursorCoelutionScore | ( | ) |
calculate the precursor cross-correlation contrast score
double calcXcorrPrecursorCombinedCoelutionScore | ( | ) |
calculate the precursor cross-correlation coelution score including the transitions
double calcXcorrPrecursorCombinedShapeScore | ( | ) |
calculate the precursor cross-correlation shape score including the transitions
double calcXcorrPrecursorContrastCoelutionScore | ( | ) |
Calculate the precursor cross-correlation contrast score against the transitions.
The score is a distance where zero indicates perfect coelution.
double calcXcorrPrecursorContrastShapeScore | ( | ) |
calculate the precursor cross-correlation shape score against the transitions
double calcXcorrPrecursorShapeScore | ( | ) |
calculate the precursor cross-correlation shape score
double calcXcorrShapeScore | ( | ) |
Calculate the cross-correlation shape score.
The score is a correlation measure where 1 indicates perfect correlation and 0 means no correlation.
double calcXcorrShapeWeightedScore | ( | const std::vector< double > & | normalized_library_intensity | ) |
Calculate the weighted cross-correlation shape score.
The score is a correlation measure where 1 indicates perfect correlation and 0 means no correlation. The score is weighted by the transition intensities, non-perfect coelution in low-intensity transitions should thus become less important.
const OpenMS::Matrix<double>& getMIContrastMatrix | ( | ) | const |
non-mutable access to the MI contrast matrix
const OpenMS::Matrix<double>& getMIMatrix | ( | ) | const |
non-mutable access to the MI matrix
const OpenMS::Matrix<double>& getMIPrecursorCombinedMatrix | ( | ) | const |
non-mutable access to the MI precursor combined matrix
const OpenMS::Matrix<double>& getMIPrecursorContrastMatrix | ( | ) | const |
non-mutable access to the MI precursor contrast matrix
const XCorrMatrixType& getXCorrContrastMatrix | ( | ) | const |
non-mutable access to the cross-correlation contrast matrix
const XCorrMatrixType& getXCorrMatrix | ( | ) | const |
non-mutable access to the cross-correlation matrix
const XCorrMatrixType& getXCorrPrecursorCombinedMatrix | ( | ) | const |
non-mutable access to the cross-correlation precursor contrast matrix
const XCorrMatrixType& getXCorrPrecursorContrastMatrix | ( | ) | const |
non-mutable access to the cross-correlation precursor contrast matrix
void initializeMIContrastMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | native_ids_set1, | ||
const std::vector< std::string > & | native_ids_set2 | ||
) |
Initialize the scoring object and building the MI matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions)
void initializeMIMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | native_ids | ||
) |
Initialize the scoring object and building the MI matrix.
void initializeMIPrecursorCombinedMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | precursor_ids, | ||
const std::vector< std::string > & | native_ids | ||
) |
Initialize the mutual information vector with the MS1 trace.
void initializeMIPrecursorContrastMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | precursor_ids, | ||
const std::vector< std::string > & | native_ids | ||
) |
Initialize the mutual information vector against the MS1 trace.
void initializeMIPrecursorMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | precursor_ids | ||
) |
Initialize the scoring object and building the MI matrix.
void initializeXCorrContrastMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | native_ids_set1, | ||
const std::vector< std::string > & | native_ids_set2 | ||
) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions)
void initializeXCorrMatrix | ( | const std::vector< std::vector< double > > & | data | ) |
Initialize the scoring object and building the cross-correlation matrix.
void initializeXCorrMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | native_ids | ||
) |
Initialize the scoring object and building the cross-correlation matrix.
void initializeXCorrPrecursorCombinedMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | precursor_ids, | ||
const std::vector< std::string > & | native_ids | ||
) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes and transitions.
void initializeXCorrPrecursorContrastMatrix | ( | const std::vector< std::vector< double > > & | data_precursor, |
const std::vector< std::vector< double > > & | data_fragments | ||
) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions.
void initializeXCorrPrecursorContrastMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | precursor_ids, | ||
const std::vector< std::string > & | native_ids | ||
) |
Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions.
void initializeXCorrPrecursorMatrix | ( | OpenSwath::IMRMFeature * | mrmfeature, |
const std::vector< std::string > & | precursor_ids | ||
) |
Initialize the scoring object and building the cross-correlation matrix.
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private |
the precomputed contrast mutual information matrix
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private |
the precomputed mutual information matrix
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private |
the precomputed contrast mutual information matrix with the MS1 trace
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private |
the precomputed contrast mutual information matrix against the MS1 trace
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private |
the precomputed mutual information matrix of the MS1 trace
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private |
the precomputed contrast cross correlation
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private |
contains max Peaks from xcorr_contrast_matrix_
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private |
the precomputed cross correlation matrix
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private |
contains max Peaks from xcorr_matrix_
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private |
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private |
the precomputed cross correlation with the MS1 trace
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private |
the precomputed cross correlation against the MS1 trace
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private |
the precomputed cross correlation matrix of the MS1 trace