Calculates an FDR from identifications. More...

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

Inheritance diagram for FalseDiscoveryRate:

Public Member Functions
	FalseDiscoveryRate ()
	Default constructor. More...

void	apply (std::vector< PeptideIdentification > &fwd_ids, std::vector< PeptideIdentification > &rev_ids) const
	Calculates the FDR of two runs, a forward run and a decoy run on peptide level. More...

void	apply (std::vector< PeptideIdentification > &id) const
	Calculates the FDR of one run from a concatenated sequence db search. More...

void	apply (std::vector< ProteinIdentification > &fwd_ids, std::vector< ProteinIdentification > &rev_ids) const
	Calculates the FDR of two runs, a forward run and decoy run on protein level. More...

void	apply (std::vector< ProteinIdentification > &ids) const
	Calculate the FDR of one run from a concatenated sequence db search. 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 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...

Private Member Functions
	FalseDiscoveryRate (const FalseDiscoveryRate &)
	Not implemented. More...

FalseDiscoveryRate &	operator= (const FalseDiscoveryRate &)
	Not implemented. More...

void	calculateFDRs_ (Map< double, double > &score_to_fdr, std::vector< double > &target_scores, std::vector< double > &decoy_scores, bool q_value, bool higher_score_better) const
	calculates the fdr stored into fdrs, given two vectors of scores More...

Additional Inherited Members
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...

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

Calculates an FDR from identifications.

Either two runs of forward and decoy database identification or one run containing both (with marks) can be used to annotate each of the peptide hits with a FDR.

Also q-values can be reported instead of p-values. q-values are basically only adjusted p-values, also ranging from 0 to 1, with lower values being preferable. When looking at the list of hits ordered by q-values, then a hit with q-value of x means that there is an x*100 percent chance that all hits with a q-value <= x are a false positive hit.

Todo:: implement combined searches properly (Andreas)

Improvement:: implement charge state separated fdr/q-values (Andreas)

Parameters of this class are:

Name	Type	Default	Restrictions	Description
no_qvalues	string	false	true, false	If 'true' strict FDRs will be calculated instead of q-values (the default)
use_all_hits	string	false	true, false	If 'true' not only the first hit, but all are used (peptides only)
split_charge_variants	string	false	true, false	If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only).
treat_runs_separately	string	false	true, false	If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only).
add_decoy_peptides	string	false	true, false	If 'true' decoy peptides will be written to output file, too. The q-value is set to the closest target score.
add_decoy_proteins	string	false	true, false	If 'true' decoy proteins will be written to output file, too. The q-value is set to the closest target score.

Note:

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

Constructor & Destructor Documentation

◆ FalseDiscoveryRate() [1/2]

FalseDiscoveryRate ( )

Default constructor.

◆ FalseDiscoveryRate() [2/2]

FalseDiscoveryRate ( const FalseDiscoveryRate & )

private

Not implemented.

Member Function Documentation

◆ apply() [1/4]

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

Calculates the FDR of two runs, a forward run and a decoy run on peptide level.

Parameters

fwd_ids	forward peptide identifications
rev_ids	reverse peptide identifications

Referenced by RNPxlSearch::main_().

◆ apply() [2/4]

void apply ( std::vector< PeptideIdentification > & id ) const

Calculates the FDR of one run from a concatenated sequence db search.

Parameters

id	peptide identifications, containing target and decoy hits

◆ apply() [3/4]

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

Calculates the FDR of two runs, a forward run and decoy run on protein level.

Parameters

fwd_ids	forward protein identifications
rev_ids	reverse protein identifications

◆ apply() [4/4]

void apply ( std::vector< ProteinIdentification > & ids ) const

Calculate the FDR of one run from a concatenated sequence db search.

Parameters

ids	protein identifications, containing target and decoy hits

◆ calculateFDRs_()

void calculateFDRs_	(	Map< double, double > &	score_to_fdr,
		std::vector< double > &	target_scores,
		std::vector< double > &	decoy_scores,
		bool	q_value,
		bool	higher_score_better
	)		const

private

calculates the fdr stored into fdrs, given two vectors of scores

◆ operator=()

FalseDiscoveryRate& operator= ( const FalseDiscoveryRate & )

private

Not implemented.

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FalseDiscoveryRate() [1/2]

◆ FalseDiscoveryRate() [2/2]

Member Function Documentation

◆ apply() [1/4]

◆ apply() [2/4]

◆ apply() [3/4]

◆ apply() [4/4]

◆ calculateFDRs_()

◆ operator=()