MRMScoring Class Reference

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

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

List of all members.

Public Types
typedef std::map< int, double >	XCorrArrayType
	Type definitions.
typedef std::vector < std::vector< XCorrArrayType > >	XCorrMatrixType
	Cross Correlation matrix.
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
Private Attributes
Members
XCorrMatrixType	xcorr_matrix_
	the precomputed cross correlation matrix
Scores
void	initializeXCorrMatrix (OpenSwath::IMRMFeature *mrmfeature, OpenSwath::ITransitionGroup *transition_group, bool normalize)
	Initialize the scoring object and building the cross-correlation matrix.
double	calcXcorrCoelutionScore ()
	calculate the cross-correlation score
double	calcXcorrShape_score ()
	calculate the cross-correlation shape score
double	calcXcorrShape_score_weighted (const std::vector< double > &normalized_library_intensity)
	calculate the weighted cross-correlation shape score
double	calcXcorrCoelutionScore_weighted (const std::vector< double > &normalized_library_intensity)
	calculate the weighted cross-correlation score
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)
static double	calcRTScore (const PeptideType &peptide, double normalized_experimental_rt)
	calculate the retention time correlation score
static double	calcSNScore (OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators)
	calculate the Signal to Noise ratio

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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, 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:

• xcorr_coelution: Crosscorrelation of the different transitions
• xcorr_shape: Crosscorrelation shape score (whether the maximal crosscorrelation 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

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Member Typedef Documentation

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

typedef OpenSwath::LightPeptide PeptideType

typedef OpenSwath::LightProtein ProteinType

typedef OpenSwath::SpectrumPtr SpectrumType

typedef std::string String

typedef OpenSwath::LightTransition TransitionType

typedef std::map<int, double> XCorrArrayType

Type definitions.

Cross Correlation array

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

Cross Correlation matrix.

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Member Function Documentation

static void calcLibraryScore	(	OpenSwath::IMRMFeature *	mrmfeature,
		const std::vector< TransitionType > &	transitions,
		double &	correlation,
		double &	rmsd,
		double &	manhattan,
		double &	dotprod
	)			[static]

calculate the library correlation score (correlation and rmsd)

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

calculate the retention time correlation score

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

double calcXcorrShape_score_weighted

(

const std::vector< double > &

normalized_library_intensity

)

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.

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Member Data Documentation

XCorrMatrixType xcorr_matrix_ [private]

the precomputed cross correlation matrix