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

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

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

Accessors
const XCorrMatrixType &	getXCorrMatrix () const
	non-mutable access to the Cross-correlation matrix More...

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

std::vector< double >	ms1_mi_vector_
	the precomputed mutual information with the MS1 trace More...

Members
XCorrMatrixType	xcorr_matrix_
	the precomputed cross correlation matrix More...

std::vector< XCorrArrayType >	ms1_xcorr_vector_
	the precomputed cross correlation with the MS1 trace More...

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

void	initializeMS1XCorr (OpenSwath::IMRMFeature *mrmfeature, const std::vector< String > &native_ids, const std::string &precursor_id)
	Initialize the cross-correlation vector with the MS1 trace. More...

void	initializeXCorrIdMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< String > &native_ids_identification, const std::vector< String > &native_ids_detection)
	Initialize the scoring object and building the cross-correlation matrix of identification vs detection chromatograms. More...

double	calcXcorrCoelutionScore ()
	calculate the cross-correlation score More...

std::string	calcIndXcorrIdCoelutionScore ()

double	calcXcorrShape_score ()
	calculate the cross-correlation shape score More...

std::string	calcIndXcorrIdShape_score ()

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...

double	calcMS1XcorrCoelutionScore ()
	calculate the MS1 cross-correlation score More...

double	calcMS1XcorrShape_score ()
	calculate the MS1 cross-correlation shape score More...

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

void	initializeMS1MI (OpenSwath::IMRMFeature *mrmfeature, std::vector< String > native_ids, std::string precursor_id)
	Initialize the mutual information vector with the MS1 trace. More...

void	initializeMIIdMatrix (OpenSwath::IMRMFeature *mrmfeature, std::vector< String > native_ids_identification, std::vector< String > native_ids_detection)
	Initialize the scoring object and building the mutual information matrix of identification vs detection chromatograms. More...

double	calcMIScore ()

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

double	calcMS1MIScore ()

std::string	calcIndMIIdScore ()

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::string	calcIndSNScore (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

◆ calcIndMIIdScore()

std::string calcIndMIIdScore ( )

◆ calcIndSNScore()

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

static

◆ calcIndXcorrIdCoelutionScore()

std::string calcIndXcorrIdCoelutionScore ( )

◆ calcIndXcorrIdShape_score()

std::string calcIndXcorrIdShape_score ( )

◆ 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

◆ calcMIScore()

double calcMIScore ( )

◆ calcMIScore_weighted()

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

◆ calcMS1MIScore()

double calcMS1MIScore ( )

◆ calcMS1XcorrCoelutionScore()

double calcMS1XcorrCoelutionScore ( )

calculate the MS1 cross-correlation score

◆ calcMS1XcorrShape_score()

double calcMS1XcorrShape_score ( )

calculate the MS1 cross-correlation shape score

◆ calcRTScore()

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

static

calculate the retention time correlation 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 score

◆ calcXcorrCoelutionScore_weighted()

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

calculate the weighted cross-correlation score

◆ calcXcorrShape_score()

double calcXcorrShape_score ( )

calculate the cross-correlation shape score

◆ calcXcorrShape_score_weighted()

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

calculate the weighted cross-correlation shape score

◆ getMIMatrix()

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

non-mutable access to the MI matrix

◆ getXCorrMatrix()

const XCorrMatrixType& getXCorrMatrix ( ) const

non-mutable access to the Cross-correlation matrix

◆ initializeMIIdMatrix()

void initializeMIIdMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< String >	native_ids_identification,
		std::vector< String >	native_ids_detection
	)

Initialize the scoring object and building the mutual information matrix of identification vs detection chromatograms.

◆ initializeMIMatrix()

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

Initialize the scoring object and building the MI matrix.

◆ initializeMS1MI()

void initializeMS1MI	(	OpenSwath::IMRMFeature *	mrmfeature,
		std::vector< String >	native_ids,
		std::string	precursor_id
	)

Initialize the mutual information vector with the MS1 trace.

◆ initializeMS1XCorr()

void initializeMS1XCorr	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	native_ids,
		const std::string &	precursor_id
	)

Initialize the cross-correlation vector with the MS1 trace.

◆ initializeXCorrIdMatrix()

void initializeXCorrIdMatrix	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< String > &	native_ids_identification,
		const std::vector< String > &	native_ids_detection
	)

Initialize the scoring object and building the cross-correlation matrix of identification vs detection chromatograms.

◆ initializeXCorrMatrix()

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

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

Member Data Documentation

◆ mi_matrix_

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

private

the precomputed mutual information matrix

◆ ms1_mi_vector_

std::vector<double> ms1_mi_vector_

private

the precomputed mutual information with the MS1 trace

◆ ms1_xcorr_vector_

std::vector<XCorrArrayType> ms1_xcorr_vector_

private

the precomputed cross correlation with the MS1 trace

◆ xcorr_matrix_

XCorrMatrixType xcorr_matrix_

private

the precomputed cross correlation matrix

Public Types

Public Member Functions

Private Attributes

Scores

Detailed Description

Member Typedef Documentation

◆ FeatureType

◆ PeptideType

◆ ProteinType

◆ SpectrumType

◆ String

◆ TransitionType

◆ XCorrArrayType

◆ XCorrMatrixType

Member Function Documentation

◆ calcIndMIIdScore()

◆ calcIndSNScore()

◆ calcIndXcorrIdCoelutionScore()

◆ calcIndXcorrIdShape_score()

◆ calcLibraryScore()

◆ calcMIScore()

◆ calcMIScore_weighted()

◆ calcMS1MIScore()

◆ calcMS1XcorrCoelutionScore()

◆ calcMS1XcorrShape_score()

◆ calcRTScore()

◆ calcSNScore()

◆ calcXcorrCoelutionScore()

◆ calcXcorrCoelutionScore_weighted()

◆ calcXcorrShape_score()

◆ calcXcorrShape_score_weighted()

◆ getMIMatrix()

◆ getXCorrMatrix()

◆ initializeMIIdMatrix()

◆ initializeMIMatrix()

◆ initializeMS1MI()

◆ initializeMS1XCorr()

◆ initializeXCorrIdMatrix()

◆ initializeXCorrMatrix()

Member Data Documentation

◆ mi_matrix_

◆ ms1_mi_vector_

◆ ms1_xcorr_vector_

◆ xcorr_matrix_