OpenSwathScoring Class Reference

A class that calls the scoring routines. More...

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>

Public Member Functions
	OpenSwathScoring ()
	Constructor. More...
	~OpenSwathScoring ()
	Destructor. More...
void	initialize (double rt_normalization_factor, int add_up_spectra, double spacing_for_spectra_resampling, OpenSwath_Scores_Usage &su)
	Initialize the scoring object. More...
void	calculateChromatographicScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< std::string > &native_ids, const std::vector< double > &normalized_library_intensity, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators, OpenSwath_Scores &scores)
	Score a single peakgroup in a chromatogram using only chromatographic properties. More...
void	calculateLibraryScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, const PeptideType &pep, const double normalized_feature_rt, OpenSwath_Scores &scores)
	Score a single chromatographic feature against a spectral library. More...
void	calculateDIAScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, OpenSwath::SpectrumAccessPtr swath_map, OpenSwath::SpectrumAccessPtr ms1_map, OpenMS::DIAScoring &diascoring, const PeptideType &pep, OpenSwath_Scores &scores)
	Score a single chromatographic feature using DIA / SWATH scores. More...
void	getNormalized_library_intensities_ (const std::vector< TransitionType > &transitions, std::vector< double > &normalized_library_intensity)
	Computing the normalized library intensities from the transition objects. More...
OpenSwath::SpectrumPtr	getAddedSpectra_ (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add)
	Returns an averaged spectrum. More...

Private Types
typedef OpenSwath::LightPeptide	PeptideType
typedef OpenSwath::LightTransition	TransitionType

Private Attributes
double	rt_normalization_factor_
int	add_up_spectra_
double	spacing_for_spectra_resampling_
OpenSwath_Scores_Usage	su_

Detailed Description

A class that calls the scoring routines.

Use this class to invoke the individual OpenSWATH scoring routines.

Member Typedef Documentation

typedef OpenSwath::LightPeptide PeptideType

private

typedef OpenSwath::LightTransition TransitionType

private

Constructor & Destructor Documentation

OpenSwathScoring

(

)

Constructor.

~OpenSwathScoring

(

)

Destructor.

Member Function Documentation

void calculateChromatographicScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< std::string > &	native_ids,
		const std::vector< double > &	normalized_library_intensity,
		std::vector< OpenSwath::ISignalToNoisePtr > &	signal_noise_estimators,
		OpenSwath_Scores &	scores
	)

Score a single peakgroup in a chromatogram using only chromatographic properties.

This function only uses the chromatographic properties (coelution, signal to noise, etc.) of a peakgroup in a chromatogram to compute scores. If more information is available, also consider using the library based scoring and the full-spectrum based scoring.

The scores are returned in the OpenSwath_Scores object. Only those scores specified in the OpenSwath_Scores_Usage object are computed.

Parameters

imrmfeature	The feature to be scored
native_ids	The list of native ids (giving a canonical ordering of the transitions)
normalized_library_intensity	The weights to be used for each transition (e.g. normalized library intensities)
signal_noise_estimators	The signal-to-noise estimators for each transition
scores	The object to store the result

void calculateDIAScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< TransitionType > &	transitions,
		OpenSwath::SpectrumAccessPtr	swath_map,
		OpenSwath::SpectrumAccessPtr	ms1_map,
		OpenMS::DIAScoring &	diascoring,
		const PeptideType &	pep,
		OpenSwath_Scores &	scores
	)

Score a single chromatographic feature using DIA / SWATH scores.

The scores are returned in the OpenSwath_Scores object.

Parameters

imrmfeature	The feature to be scored
transitions	The library transition to score the feature against
swath_map	The SWATH-MS (DIA map) from which to retrieve full MS/MS spectra at the chromatographic peak apices
ms1_map	The corresponding MS1 (precursor ion map) from which the precursor spectra can be retrieved (optional, may be NULL)
diascoring	DIA Scoring object to use for scoring
pep	The peptide corresponding to the library transitions
scores	The object to store the result

void calculateLibraryScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< TransitionType > &	transitions,
		const PeptideType &	pep,
		const double	normalized_feature_rt,
		OpenSwath_Scores &	scores
	)

Score a single chromatographic feature against a spectral library.

The spectral library is provided in a set of transition objects and a peptide object. Both contain information about the expected elution time on the chromatography and the relative intensity of the transitions.

The scores are returned in the OpenSwath_Scores object.

Parameters

imrmfeature	The feature to be scored
transitions	The library transition to score the feature against
pep	The peptide corresponding to the library transitions
normalized_feature_rt	The retention time of the feature in normalized space
scores	The object to store the result

OpenSwath::SpectrumPtr getAddedSpectra_	(	OpenSwath::SpectrumAccessPtr	swath_map,
		double	RT,
		int	nr_spectra_to_add
	)

Returns an averaged spectrum.

This function will sum up (add) the intensities of multiple spectra around the given retention time and return an "averaged" spectrum which may contain less noise.

Parameters

swath_map	The map containing the spectra
RT	The target retention time
nr_spectra_to_add	How many spectra to add up

void getNormalized_library_intensities_	(	const std::vector< TransitionType > &	transitions,
		std::vector< double > &	normalized_library_intensity
	)

Computing the normalized library intensities from the transition objects.

The intensities are normalized such that the sum to one.

Parameters

transitions	The library transition to score the feature against
normalized_library_intensity	The resulting normalized library intensities

void initialize	(	double	rt_normalization_factor,
		int	add_up_spectra,
		double	spacing_for_spectra_resampling,
		OpenSwath_Scores_Usage &	su
	)

Initialize the scoring object.

Sets the parameters for the scoring.

Parameters

rt_normalization_factor	Specifies the range of the normalized retention time space
add_up_spectra	How many spectra to add up (default 1)
spacing_for_spectra_resampling	Spacing factor for spectra addition
su	Which scores to actually compute

Member Data Documentation

int add_up_spectra_

private

double rt_normalization_factor_

private

double spacing_for_spectra_resampling_

private

OpenSwath_Scores_Usage su_

private