IDDecoyProbability Class Reference

IDDecoyProbability calculates probabilities using decoy approach. More...

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

Inheritance diagram for IDDecoyProbability:

Collaboration diagram for IDDecoyProbability:

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.
	~IDDecoyProbability () override
	Destructor.
IDDecoyProbability &	operator= (const IDDecoyProbability &rhs)
	assignment operator
void	apply (PeptideIdentificationList &prob_ids, const PeptideIdentificationList &fwd_ids, const PeptideIdentificationList &rev_ids)
	Converts the forward and reverse identification into probabilities.
void	apply (PeptideIdentificationList &ids)
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Protected Member Functions
void	normalizeBins_ (const std::vector< double > &scores, std::vector< double > &binned, Transformation_ &trafo)
double	getProbability_ (const Math::GammaDistributionFitter::GammaDistributionFitResult &result_gamma, const Transformation_ &gamma_trafo, const Math::GaussFitter::GaussFitResult &result_gauss, const Transformation_ &gauss_trafo, double score)
void	generateDistributionImage_ (const std::vector< double > &ids, const std::string &formula, const std::string &filename)
void	generateDistributionImage_ (const std::vector< double > &all_ids, const Transformation_ &all_trans, const std::string &fwd_formula, const std::string &rev_formula, const std::string &filename)
void	apply_ (PeptideIdentificationList &ids, const std::vector< double > &rev_scores, const std::vector< double > &fwd_scores, const std::vector< double > &all_scores)
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.
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

IDDecoyProbability calculates probabilities using decoy approach.

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

Parameters of this class are:

Name	Type	Default	Restrictions	Description
number_of_bins	int	40		Number of bins used for the fitting, if sparse datasets are used, this number should be smaller
lower_score_better_default_value_if_zero	float	50.0		This value is used if e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)

Note:

• If a section name is documented, the documentation is displayed as tooltip.
• Advanced parameter names are italic.

Constructor & Destructor Documentation

IDDecoyProbability() [1/2]

IDDecoyProbability

(

)

Default constructor.

IDDecoyProbability() [2/2]

IDDecoyProbability

(

const IDDecoyProbability &

rhs

)

Copy constructor.

~IDDecoyProbability()

~IDDecoyProbability ( )

override

Destructor.

Member Function Documentation

apply() [1/2]

void apply

(

PeptideIdentificationList &

ids

)

apply() [2/2]

void apply	(	PeptideIdentificationList &	prob_ids,
		const PeptideIdentificationList &	fwd_ids,
		const PeptideIdentificationList &	rev_ids
	)

Converts the forward and reverse identification into probabilities.

  @param[out] prob_ids Output of the algorithm which includes identifications with probability based scores
  @param[in] fwd_ids Input parameter which represents the identifications of the forward search
  @param[in] rev_ids Input parameter which represents the identifications of the reversed search

apply_()

void apply_ ( PeptideIdentificationList &  ids, const std::vector< double > &  rev_scores, const std::vector< double > &  fwd_scores, const std::vector< double > &  all_scores  )

protected

generateDistributionImage_() [1/2]

void generateDistributionImage_ ( const std::vector< double > &  all_ids, const Transformation_ &  all_trans, const std::string &  fwd_formula, const std::string &  rev_formula, const std::string &  filename  )

protected

generateDistributionImage_() [2/2]

void generateDistributionImage_ ( const std::vector< double > &  ids, const std::string &  formula, const std::string &  filename  )

protected

getProbability_()

double getProbability_ ( const Math::GammaDistributionFitter::GammaDistributionFitResult &  result_gamma, const Transformation_ &  gamma_trafo, const Math::GaussFitter::GaussFitResult &  result_gauss, const Transformation_ &  gauss_trafo, double  score  )

protected

normalizeBins_()

void normalizeBins_ ( const std::vector< double > &  scores, std::vector< double > &  binned, Transformation_ &  trafo  )

protected

operator=()

IDDecoyProbability & operator=

(

const IDDecoyProbability &

rhs

)

assignment operator