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. More...

	IDDecoyProbability (const IDDecoyProbability &rhs)
	Copy constructor. More...

	~IDDecoyProbability () override
	Destructor. More...

IDDecoyProbability &	operator= (const IDDecoyProbability &rhs)
	assignment operator More...

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. More...

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

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...

DefaultParamHandler &	operator= (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 Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () 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	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 String &formula, const String &filename)

void	generateDistributionImage_ (const std::vector< double > &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< 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. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

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< String >	subsections_
	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

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 ( std::vector< PeptideIdentification > & ids )

◆ apply() [2/2]

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.

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

◆ apply_()

void apply_	(	std::vector< PeptideIdentification > &	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 String &	fwd_formula,
		const String &	rev_formula,
		const String &	filename
	)

protected

◆ generateDistributionImage_() [2/2]

void generateDistributionImage_	(	const std::vector< double > &	ids,
		const String &	formula,
		const 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

Classes

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IDDecoyProbability() [1/2]

◆ IDDecoyProbability() [2/2]

◆ ~IDDecoyProbability()

Member Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ apply_()

◆ generateDistributionImage_() [1/2]

◆ generateDistributionImage_() [2/2]

◆ getProbability_()

◆ normalizeBins_()

◆ operator=()