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MRMScoring Class Reference

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

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

Public Types

typedef std::map< int, doubleXCorrArrayType
 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::LightPeptide PeptideType
 
typedef OpenSwath::LightProtein ProteinType
 
typedef boost::shared_ptr< OpenSwath::IFeatureFeatureType
 

Public Member Functions

Accessors
const XCorrMatrixTypegetXCorrMatrix () const
 non-mutable access to the Cross-correlation matrix More...
 

Private Attributes

Members
XCorrMatrixType xcorr_matrix_
 the precomputed cross correlation matrix More...
 
std::vector< XCorrArrayTypems1_xcorr_vector_
 the precomputed cross correlation with the MS1 trace More...
 

Scores

void initializeXCorrMatrix (OpenSwath::IMRMFeature *mrmfeature, std::vector< String > native_ids)
 Initialize the scoring object and building the cross-correlation matrix. More...
 
void initializeMS1XCorr (OpenSwath::IMRMFeature *mrmfeature, std::vector< String > native_ids, std::string precursor_id)
 Initialize the cross-correlation vector with the MS1 trace. More...
 
double calcXcorrCoelutionScore ()
 calculate the cross-correlation score More...
 
double calcXcorrShape_score ()
 calculate the cross-correlation shape score More...
 
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...
 
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...
 

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:

Member Typedef Documentation

typedef boost::shared_ptr<OpenSwath::IFeature> FeatureType
typedef std::string String
typedef std::map<int, double> XCorrArrayType

Type definitions.

Cross Correlation array

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

Cross Correlation matrix.

Member Function Documentation

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

double calcMS1XcorrCoelutionScore ( )

calculate the MS1 cross-correlation score

double calcMS1XcorrShape_score ( )

calculate the MS1 cross-correlation shape score

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-mutable access to the Cross-correlation matrix

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

Initialize the cross-correlation vector with the MS1 trace.

void initializeXCorrMatrix ( OpenSwath::IMRMFeature mrmfeature,
std::vector< String native_ids 
)

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

Member Data Documentation

std::vector<XCorrArrayType> ms1_xcorr_vector_
private

the precomputed cross correlation with the MS1 trace

XCorrMatrixType xcorr_matrix_
private

the precomputed cross correlation matrix


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:31 using doxygen 1.8.11