This class implements different scores for peaks found in SRM/MRM. More...

#include <OpenMS/OPENSWATHALGO/ALGO/MRMScoring.h>

Collaboration diagram for MRMScoring:

Public Types
typedef OpenSwath::Scoring::XCorrArrayType	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::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...

XCorrMatrixType	xcorr_contrast_matrix_
	the precomputed contrast cross correlation 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...

std::vector< std::vector< double > >	mi_matrix_
	the precomputed mutual information matrix More...

std::vector< std::vector< double > >	mi_contrast_matrix_
	the precomputed contrast mutual information matrix More...

std::vector< std::vector< double > >	mi_precursor_matrix_
	the precomputed mutual information matrix of the MS1 trace More...

std::vector< std::vector< double > >	mi_precursor_contrast_matrix_
	the precomputed contrast mutual information matrix against the MS1 trace More...

std::vector< std::vector< 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< String > &native_ids)
	Initialize the scoring object and building the cross-correlation matrix. More...

void	initializeXCorrContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< String > &native_ids_set1, const std::vector< 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< String > &precursor_ids)
	Initialize the scoring object and building the cross-correlation matrix. More...

void	initializeXCorrPrecursorContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< String > &precursor_ids, const std::vector< 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< String > &precursor_ids, const std::vector< 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 std::vector< std::vector< double > > &	getMIMatrix () const
	non-mutable access to the MI matrix More...

const std::vector< std::vector< double > > &	getMIContrastMatrix () const
	non-mutable access to the MI contrast matrix More...

const std::vector< std::vector< double > > &	getMIPrecursorContrastMatrix () const
	non-mutable access to the MI precursor contrast matrix More...

const std::vector< std::vector< double > > &	getMIPrecursorCombinedMatrix () const
	non-mutable access to the MI precursor combined matrix More...

void	initializeMIMatrix (OpenSwath::IMRMFeature *mrmfeature, std::vector< String > native_ids)
	Initialize the scoring object and building the MI matrix. More...

void	initializeMIContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, std::vector< String > native_ids_set1, std::vector< 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, std::vector< String > precursor_ids)
	Initialize the scoring object and building the MI matrix. More...

void	initializeMIPrecursorContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< String > &precursor_ids, const std::vector< String > &native_ids)
	Initialize the mutual information vector against the MS1 trace. More...

void	initializeMIPrecursorCombinedMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< String > &precursor_ids, const std::vector< 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)

Detailed Description

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:

xcorr_coelution: Cross-correlation of the different transitions
xcorr_shape: Cross-correlation shape score (whether the maximal Cross-correlation coincides with the maximal intensity)
library_rmsd: normalized RMSD of the measured intensities to the expected intensities
library_correlation: correlation of the measured intensities to the expected intensities
rt_score: deviation from the expected retention time
elution_fit_score: how well the elution profile fits a theoretical elution profile

Member Typedef Documentation

◆ FeatureType

typedef boost::shared_ptr<OpenSwath::IFeature> FeatureType

◆ PeptideType

typedef OpenSwath::LightCompound PeptideType

◆ ProteinType

typedef OpenSwath::LightProtein ProteinType

◆ SpectrumType

typedef OpenSwath::SpectrumPtr SpectrumType

◆ String

typedef std::string String

◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

◆ XCorrArrayType

typedef OpenSwath::Scoring::XCorrArrayType XCorrArrayType

Type definitions.

Cross Correlation array

◆ XCorrMatrixType

typedef std::vector<std::vector<XCorrArrayType> > XCorrMatrixType

Cross Correlation matrix.

Member Function Documentation

◆ calcLibraryScore()

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
	)

static

calculate the library correlation score

◆ calcMIPrecursorCombinedScore()

double calcMIPrecursorCombinedScore ( )

◆ calcMIPrecursorContrastScore()

double calcMIPrecursorContrastScore ( )

◆ calcMIPrecursorScore()

double calcMIPrecursorScore ( )

◆ calcMIScore()

double calcMIScore ( )

◆ calcMIWeightedScore()

double calcMIWeightedScore ( const std::vector< double > & normalized_library_intensity )

◆ calcRTScore()

static double calcRTScore	(	const PeptideType &	peptide,
		double	normalized_experimental_rt
	)

static

calculate the retention time correlation score

◆ calcSeparateMIContrastScore()

std::vector<double> calcSeparateMIContrastScore ( )

◆ calcSeparateSNScore()

static std::vector<double> calcSeparateSNScore	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< OpenSwath::ISignalToNoisePtr > &	signal_noise_estimators
	)

static

◆ calcSeparateXcorrContrastCoelutionScore()

std::vector<double> calcSeparateXcorrContrastCoelutionScore ( )

calculate the separate cross-correlation contrast score

◆ calcSeparateXcorrContrastShapeScore()

std::vector<double> calcSeparateXcorrContrastShapeScore ( )

calculate the separate cross-correlation contrast shape score

◆ calcSNScore()

static double calcSNScore	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< OpenSwath::ISignalToNoisePtr > &	signal_noise_estimators
	)

static

calculate the Signal to Noise ratio

◆ calcXcorrCoelutionScore()

double calcXcorrCoelutionScore ( )

Calculate the cross-correlation coelution score.

The score is a distance where zero indicates perfect coelution.

◆ calcXcorrCoelutionWeightedScore()

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.

◆ calcXcorrContrastCoelutionScore()

double calcXcorrContrastCoelutionScore ( )

calculate the cross-correlation contrast score

◆ calcXcorrContrastShapeScore()

double calcXcorrContrastShapeScore ( )

calculate the cross-correlation contrast shape score

◆ calcXcorrPrecursorCoelutionScore()

double calcXcorrPrecursorCoelutionScore ( )

calculate the precursor cross-correlation contrast score

◆ calcXcorrPrecursorCombinedCoelutionScore()

double calcXcorrPrecursorCombinedCoelutionScore ( )

calculate the precursor cross-correlation coelution score including the transitions

◆ calcXcorrPrecursorCombinedShapeScore()

double calcXcorrPrecursorCombinedShapeScore ( )

calculate the precursor cross-correlation shape score including the transitions

◆ calcXcorrPrecursorContrastCoelutionScore()

double calcXcorrPrecursorContrastCoelutionScore ( )

Calculate the precursor cross-correlation contrast score against the transitions.

The score is a distance where zero indicates perfect coelution.

◆ calcXcorrPrecursorContrastShapeScore()

double calcXcorrPrecursorContrastShapeScore ( )

calculate the precursor cross-correlation shape score against the transitions

◆ calcXcorrPrecursorShapeScore()

double calcXcorrPrecursorShapeScore ( )

calculate the precursor cross-correlation shape score

◆ calcXcorrShapeScore()

double calcXcorrShapeScore ( )

Calculate the cross-correlation shape score.

The score is a correlation measure where 1 indicates perfect correlation and 0 means no correlation.

◆ calcXcorrShapeWeightedScore()

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.

◆ getMIContrastMatrix()

const std::vector< std::vector<double> >& getMIContrastMatrix ( ) const

non-mutable access to the MI contrast matrix

◆ getMIMatrix()

const std::vector< std::vector<double> >& getMIMatrix ( ) const

non-mutable access to the MI matrix

◆ getMIPrecursorCombinedMatrix()

const std::vector< std::vector<double> >& getMIPrecursorCombinedMatrix ( ) const

non-mutable access to the MI precursor combined matrix

◆ getMIPrecursorContrastMatrix()

const std::vector< std::vector<double> >& getMIPrecursorContrastMatrix ( ) const

non-mutable access to the MI precursor contrast matrix

◆ getXCorrContrastMatrix()

const XCorrMatrixType& getXCorrContrastMatrix ( ) const

non-mutable access to the cross-correlation contrast matrix

◆ getXCorrMatrix()

const XCorrMatrixType& getXCorrMatrix ( ) const

non-mutable access to the cross-correlation matrix

◆ getXCorrPrecursorCombinedMatrix()

const XCorrMatrixType& getXCorrPrecursorCombinedMatrix ( ) const

non-mutable access to the cross-correlation precursor contrast matrix

◆ getXCorrPrecursorContrastMatrix()

const XCorrMatrixType& getXCorrPrecursorContrastMatrix ( ) const

non-mutable access to the cross-correlation precursor contrast matrix

◆ initializeMIContrastMatrix()

void initializeMIContrastMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< String >	native_ids_set1,
		std::vector< 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)

◆ initializeMIMatrix()

void initializeMIMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< String >	native_ids
	)

Initialize the scoring object and building the MI matrix.

◆ initializeMIPrecursorCombinedMatrix()

void initializeMIPrecursorCombinedMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	precursor_ids,
		const std::vector< String > &	native_ids
	)

Initialize the mutual information vector with the MS1 trace.

◆ initializeMIPrecursorContrastMatrix()

void initializeMIPrecursorContrastMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	precursor_ids,
		const std::vector< String > &	native_ids
	)

Initialize the mutual information vector against the MS1 trace.

◆ initializeMIPrecursorMatrix()

void initializeMIPrecursorMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< String >	precursor_ids
	)

Initialize the scoring object and building the MI matrix.

◆ initializeXCorrContrastMatrix()

void initializeXCorrContrastMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	native_ids_set1,
		const std::vector< 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)

◆ initializeXCorrMatrix() [1/2]

void initializeXCorrMatrix ( const std::vector< std::vector< double > > & data )

Initialize the scoring object and building the cross-correlation matrix.

◆ initializeXCorrMatrix() [2/2]

void initializeXCorrMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	native_ids
	)

Initialize the scoring object and building the cross-correlation matrix.

◆ initializeXCorrPrecursorCombinedMatrix()

void initializeXCorrPrecursorCombinedMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	precursor_ids,
		const std::vector< String > &	native_ids
	)

Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes and transitions.

◆ initializeXCorrPrecursorContrastMatrix() [1/2]

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.

◆ initializeXCorrPrecursorContrastMatrix() [2/2]

void initializeXCorrPrecursorContrastMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	precursor_ids,
		const std::vector< String > &	native_ids
	)

Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions.

◆ initializeXCorrPrecursorMatrix()

void initializeXCorrPrecursorMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	precursor_ids
	)

Initialize the scoring object and building the cross-correlation matrix.

Member Data Documentation

◆ mi_contrast_matrix_

std::vector< std::vector<double> > mi_contrast_matrix_

private

the precomputed contrast mutual information matrix

◆ mi_matrix_

std::vector< std::vector<double> > mi_matrix_

private

the precomputed mutual information matrix

◆ mi_precursor_combined_matrix_

std::vector< std::vector<double> > mi_precursor_combined_matrix_

private

the precomputed contrast mutual information matrix with the MS1 trace

◆ mi_precursor_contrast_matrix_

std::vector< std::vector<double> > mi_precursor_contrast_matrix_

private

the precomputed contrast mutual information matrix against the MS1 trace

◆ mi_precursor_matrix_

std::vector< std::vector<double> > mi_precursor_matrix_

private

the precomputed mutual information matrix of the MS1 trace

◆ xcorr_contrast_matrix_

XCorrMatrixType xcorr_contrast_matrix_

private

the precomputed contrast cross correlation

◆ xcorr_matrix_

XCorrMatrixType xcorr_matrix_

private

the precomputed cross correlation matrix

◆ xcorr_precursor_combined_matrix_

XCorrMatrixType xcorr_precursor_combined_matrix_

private

the precomputed cross correlation with the MS1 trace

◆ xcorr_precursor_contrast_matrix_

XCorrMatrixType xcorr_precursor_contrast_matrix_

private

the precomputed cross correlation against the MS1 trace

◆ xcorr_precursor_matrix_

XCorrMatrixType xcorr_precursor_matrix_

private

the precomputed cross correlation matrix of the MS1 trace

Public Types

Public Member Functions

Private Attributes

Scores

Detailed Description

Member Typedef Documentation

◆ FeatureType

◆ PeptideType

◆ ProteinType

◆ SpectrumType

◆ String

◆ TransitionType

◆ XCorrArrayType

◆ XCorrMatrixType

Member Function Documentation

◆ calcLibraryScore()

◆ calcMIPrecursorCombinedScore()

◆ calcMIPrecursorContrastScore()

◆ calcMIPrecursorScore()

◆ calcMIScore()

◆ calcMIWeightedScore()

◆ calcRTScore()

◆ calcSeparateMIContrastScore()

◆ calcSeparateSNScore()

◆ calcSeparateXcorrContrastCoelutionScore()

◆ calcSeparateXcorrContrastShapeScore()

◆ calcSNScore()

◆ calcXcorrCoelutionScore()

◆ calcXcorrCoelutionWeightedScore()

◆ calcXcorrContrastCoelutionScore()

◆ calcXcorrContrastShapeScore()

◆ calcXcorrPrecursorCoelutionScore()

◆ calcXcorrPrecursorCombinedCoelutionScore()

◆ calcXcorrPrecursorCombinedShapeScore()

◆ calcXcorrPrecursorContrastCoelutionScore()

◆ calcXcorrPrecursorContrastShapeScore()

◆ calcXcorrPrecursorShapeScore()

◆ calcXcorrShapeScore()

◆ calcXcorrShapeWeightedScore()

◆ getMIContrastMatrix()

◆ getMIMatrix()

◆ getMIPrecursorCombinedMatrix()

◆ getMIPrecursorContrastMatrix()

◆ getXCorrContrastMatrix()

◆ getXCorrMatrix()

◆ getXCorrPrecursorCombinedMatrix()

◆ getXCorrPrecursorContrastMatrix()

◆ initializeMIContrastMatrix()

◆ initializeMIMatrix()

◆ initializeMIPrecursorCombinedMatrix()

◆ initializeMIPrecursorContrastMatrix()

◆ initializeMIPrecursorMatrix()

◆ initializeXCorrContrastMatrix()

◆ initializeXCorrMatrix() [1/2]

◆ initializeXCorrMatrix() [2/2]

◆ initializeXCorrPrecursorCombinedMatrix()

◆ initializeXCorrPrecursorContrastMatrix() [1/2]

◆ initializeXCorrPrecursorContrastMatrix() [2/2]

◆ initializeXCorrPrecursorMatrix()

Member Data Documentation

◆ mi_contrast_matrix_

◆ mi_matrix_

◆ mi_precursor_combined_matrix_

◆ mi_precursor_contrast_matrix_

◆ mi_precursor_matrix_

◆ xcorr_contrast_matrix_

◆ xcorr_matrix_

◆ xcorr_precursor_combined_matrix_

◆ xcorr_precursor_contrast_matrix_

◆ xcorr_precursor_matrix_