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PILISScoring Class Reference

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

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

Inheritance diagram for PILISScoring:
DefaultParamHandler

Public Member Functions

PILISScoringoperator= (const PILISScoring &source)
 
constructors and destructors
 PILISScoring ()
 default constructor More...
 
 PILISScoring (const PILISScoring &source)
 copy constructor More...
 
virtual ~PILISScoring ()
 destructor More...
 
Accessors
void getScores (std::vector< PeptideIdentification > &ids)
 performs an ProteinIdentification run on a PeakMap More...
 
void getScore (PeptideIdentification &id)
 performs an ProteinIdentification run on a PeakSpectrum More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Protected Member Functions

void getFitParameter_ (double &slope, double &intercept, const std::vector< double > &scores, double threshold)
 
void getSurvivalFunction_ (Map< UInt, double > &points, std::vector< DPosition< 2 > > &survival_function)
 
void getScore_ (PeptideIdentification &id, double global_slope, double global_intercept)
 
- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Additional Inherited Members

- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

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.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
use_local_scoring int1  If set to 1, a E-Value of an identification run of one spectrum is used additionally
survival_function_bin_size int20  Bin size of the survival function
global_linear_fitting_threshold float0.1  Fitting threshold of the survival function of the global E-Value calculation
local_linear_fitting_threshold float0.5  Fitting threshold of the survival function of the local E-Value calculation
score_default_value float100000000000  If no score can be assigned use this one

Note:

Constructor & Destructor Documentation

default constructor

PILISScoring ( const PILISScoring source)

copy constructor

virtual ~PILISScoring ( )
virtual

destructor

Member Function Documentation

void getFitParameter_ ( double slope,
double intercept,
const std::vector< double > &  scores,
double  threshold 
)
protected
void getScore ( PeptideIdentification id)

performs an ProteinIdentification run on a PeakSpectrum

void getScore_ ( PeptideIdentification id,
double  global_slope,
double  global_intercept 
)
protected
void getScores ( std::vector< PeptideIdentification > &  ids)

performs an ProteinIdentification run on a PeakMap

void getSurvivalFunction_ ( Map< UInt, double > &  points,
std::vector< DPosition< 2 > > &  survival_function 
)
protected
PILISScoring& operator= ( const PILISScoring source)

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5