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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::IFeature
FeatureType
 

Public Member Functions

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

Private Attributes

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

Scores

void initializeXCorrMatrix (OpenSwath::IMRMFeature *mrmfeature, OpenSwath::ITransitionGroup *transition_group, bool normalize)
 Initialize the scoring object and building the cross-correlation matrix. 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...
 
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) 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, 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:

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 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.

Member Data Documentation

XCorrMatrixType xcorr_matrix_
private

the precomputed cross correlation matrix


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:38 using doxygen 1.8.5