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IDDecoyProbability Class Reference
[Identification]

IDDecoyProbability calculates probabilities using decoy approach. More...

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

Inheritance diagram for IDDecoyProbability:
DefaultParamHandler

List of all members.

Classes

struct  Transformation_
 struct to be used to store a transformation (used for fitting) More...

Public Member Functions

 IDDecoyProbability ()
 Default constructor.
 IDDecoyProbability (const IDDecoyProbability &rhs)
 Copy constructor.
virtual ~IDDecoyProbability ()
 Desctructor.
IDDecoyProbability & operator= (const IDDecoyProbability &rhs)
 assignment operator
void apply (std::vector< PeptideIdentification > &prob_ids, const std::vector< PeptideIdentification > &fwd_ids, const std::vector< PeptideIdentification > &rev_ids)
void apply (std::vector< PeptideIdentification > &ids)

Protected Member Functions

void normalizeBins_ (const std::vector< DoubleReal > &scores, std::vector< DoubleReal > &binned, Transformation_ &trafo)
DoubleReal getProbability_ (const Math::GammaDistributionFitter::GammaDistributionFitResult &result_gamma, const Transformation_ &gamma_trafo, const Math::GaussFitter::GaussFitResult &result_gauss, const Transformation_ &gauss_trafo, DoubleReal score)
void generateDistributionImage_ (const std::vector< DoubleReal > &ids, const String &formula, const String &filename)
void generateDistributionImage_ (const std::vector< DoubleReal > &all_ids, const Transformation_ &all_trans, const String &fwd_formula, const String &rev_formula, const String &filename)
void apply_ (std::vector< PeptideIdentification > &ids, const std::vector< DoubleReal > &rev_scores, const std::vector< DoubleReal > &fwd_scores, const std::vector< DoubleReal > &all_scores)

Detailed Description

IDDecoyProbability calculates probabilities using decoy approach.

This class calcalates the probabilities using a target deocy approach. Like in peptide prophet the forward distribution is modeled using a gaussian distribution the reverse scores are modeled using a gamma distribution.

Constructor & Destructor Documentation

IDDecoyProbability (  ) 

Default constructor.

IDDecoyProbability ( const IDDecoyProbability &  rhs  ) 

Copy constructor.

virtual ~IDDecoyProbability (  )  [virtual]

Desctructor.

Member Function Documentation

void apply ( std::vector< PeptideIdentification > &  prob_ids,
const std::vector< PeptideIdentification > &  fwd_ids,
const std::vector< PeptideIdentification > &  rev_ids 
)

converts the forward and reverse identification into probabilities

Parameters:
prob_ids Output of the algorithm which includes identifications with probability based scores
fwd_ids Input parameter which represents the identifications of the forward search
rev_ids Input parameter which represents the identifications of the reversed search
void apply ( std::vector< PeptideIdentification > &  ids  ) 
void apply_ ( std::vector< PeptideIdentification > &  ids,
const std::vector< DoubleReal > &  rev_scores,
const std::vector< DoubleReal > &  fwd_scores,
const std::vector< DoubleReal > &  all_scores 
) [protected]
void generateDistributionImage_ ( const std::vector< DoubleReal > &  all_ids,
const Transformation_ &  all_trans,
const String &  fwd_formula,
const String &  rev_formula,
const String &  filename 
) [protected]
void generateDistributionImage_ ( const std::vector< DoubleReal > &  ids,
const String &  formula,
const String &  filename 
) [protected]
DoubleReal getProbability_ ( const Math::GammaDistributionFitter::GammaDistributionFitResult &  result_gamma,
const Transformation_ &  gamma_trafo,
const Math::GaussFitter::GaussFitResult &  result_gauss,
const Transformation_ &  gauss_trafo,
DoubleReal  score 
) [protected]
void normalizeBins_ ( const std::vector< DoubleReal > &  scores,
std::vector< DoubleReal > &  binned,
Transformation_ &  trafo 
) [protected]
IDDecoyProbability& operator= ( const IDDecoyProbability &  rhs  ) 

assignment operator

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1