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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

Constructor & Destructor Documentation

Constructor.

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
imrmfeatureThe feature to be scored
native_idsThe list of native ids (giving a canonical ordering of the transitions)
normalized_library_intensityThe weights to be used for each transition (e.g. normalized library intensities)
signal_noise_estimatorsThe signal-to-noise estimators for each transition
scoresThe 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
imrmfeatureThe feature to be scored
transitionsThe library transition to score the feature against
swath_mapThe SWATH-MS (DIA map) from which to retrieve full MS/MS spectra at the chromatographic peak apices
ms1_mapThe corresponding MS1 (precursor ion map) from which the precursor spectra can be retrieved (optional, may be NULL)
diascoringDIA Scoring object to use for scoring
pepThe peptide corresponding to the library transitions
scoresThe 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
imrmfeatureThe feature to be scored
transitionsThe library transition to score the feature against
pepThe peptide corresponding to the library transitions
normalized_feature_rtThe retention time of the feature in normalized space
scoresThe 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_mapThe map containing the spectra
RTThe target retention time
nr_spectra_to_addHow 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
transitionsThe library transition to score the feature against
normalized_library_intensityThe 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_factorSpecifies the range of the normalized retention time space
add_up_spectraHow many spectra to add up (default 1)
spacing_for_spectra_resamplingSpacing factor for spectra addition
suWhich scores to actually compute

Member Data Documentation

int add_up_spectra_
private
double rt_normalization_factor_
private
double spacing_for_spectra_resampling_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:29 using doxygen 1.8.11