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PILISScoring Class Reference
[ID]

#include <OpenMS/ANALYSIS/ID/PILISScoring.h>

Inheritance diagram for PILISScoring:

DefaultParamHandler

List of all members.


Detailed Description

This class actually implements the E-value based scoring of PILIS.

The method which is used to generate the E-values are adapted from

David Fenyo and Ronald C. Beavis Anal. Chem. 2003, 75, 768-774 A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes.

The bases for the calculation are the similarity scores of the simulated and experimental spectra. The scores are tranformed into a discrete score distribution and from this distribution E-values are calculated for the peptide hits.

If more than one spectrum is given two E-values can be calculated, one which gives the significance of the peptide hit considering only one spectrum, and the other also considering also all other hits of all other spectra. The second type of scoring is somewhat more accurate.

PILISScoring Parameters are explained on a separate page.

Public Member Functions

PILISScoringoperator= (const PILISScoring &source)
constructors and destructors
 PILISScoring ()
 default constructor
 PILISScoring (const PILISScoring &source)
 copy constructor
virtual ~PILISScoring ()
 destructor
Accessors
void getScores (std::vector< PeptideIdentification > &ids)
 performs an ProteinIdentification run on a PeakMap
void getScore (PeptideIdentification &id)
 performs an ProteinIdentification run on a PeakSpectrum

Protected Member Functions

void getFitParameter_ (double &slope, double &intercept, const std::vector< double > &scores, double threshold)
void getSurvivalFunction_ (HashMap< UInt, double > &points, std::vector< DPosition< 2 > > &survival_function)
void getScore_ (PeptideIdentification &id, double global_slope, double global_intercept)


Constructor & Destructor Documentation

PILISScoring (  ) 

default constructor

PILISScoring ( const PILISScoring source  ) 

copy constructor

virtual ~PILISScoring (  )  [virtual]

destructor


Member Function Documentation

PILISScoring& operator= ( const PILISScoring source  ) 

void getScores ( std::vector< PeptideIdentification > &  ids  ) 

performs an ProteinIdentification run on a PeakMap

void getScore ( PeptideIdentification id  ) 

performs an ProteinIdentification run on a PeakSpectrum

void getFitParameter_ ( double &  slope,
double &  intercept,
const std::vector< double > &  scores,
double  threshold 
) [protected]

void getSurvivalFunction_ ( HashMap< UInt, double > &  points,
std::vector< DPosition< 2 > > &  survival_function 
) [protected]

void getScore_ ( PeptideIdentification id,
double  global_slope,
double  global_intercept 
) [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:41 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1