Calculates false discovery rate estimates on crosslink identifications. More...

#include <OpenMS/ANALYSIS/XLMS/XFDRAlgorithm.h>

Inheritance diagram for XFDRAlgorithm:

Collaboration diagram for XFDRAlgorithm:

Public Types
enum	ExitCodes { EXECUTION_OK , ILLEGAL_PARAMETERS , UNEXPECTED_RESULT }
	Exit codes. More...

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

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

	~XFDRAlgorithm () override
	Default destructor. More...

ExitCodes	run (std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id)
	Performs the main function of this class, the FDR estimation for cross-linked peptide experiments. More...

ExitCodes	validateClassArguments () const
	Checks whether the parameters of the object are valid. 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...

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	initDataStructures_ (std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id)
	Prepares vector of PeptideIdentification such that it can be processed downstream. The encompassed steps are: More...

void	fdr_xprophet_ (std::map< String, Math::Histogram<> > &cum_histograms, const String &targetclass, const String &decoyclass, const String &fulldecoyclass, std::vector< double > &fdr, bool mono) const
	xprophet method for target hits counting as implemented in xProphet More...

void	findTopUniqueHits_ (std::vector< PeptideIdentification > &peptide_ids)

void	writeArgumentsLog_ () const

String	getId_ (const PeptideHit &ph) const

Static Private Member Functions
static void	assignTypes_ (PeptideHit &pep_id, StringList &types)
	Inspects a PeptideIdentification and assigns all cross-link types that this identification belongs to. More...

static void	calc_qfdr_ (const std::vector< double > &fdr, std::vector< double > &qfdr)
	Calculates the qFDR values for the provided FDR values, assuming that the FDRs are sorted by score in the input vector. More...

static Size	getMinIonsMatched_ (const PeptideHit &ph)

static void	setIntraProtein_ (PeptideHit &ph, const bool value)

static void	setInterProtein_ (PeptideHit &ph, const bool value)

static bool	isSameProtein_ (String prot1, String prot2, const String &decoy_string)
	Determines whether the Peptide Evidences belong to the same protein, modulo decoy. More...

Private Attributes
Int	min_score_

Int	max_score_

std::vector< String >	unique_ids_

std::vector< double >	unique_id_scores_

std::map< String, std::vector< String > >	cross_link_classes_

String	decoy_string_

double	arg_mindeltas_

double	arg_minborder_

double	arg_maxborder_

Int	arg_minionsmatched_

double	arg_minscore_

bool	arg_uniquex_

bool	arg_no_qvalues_

double	arg_binsize_

Static Private Attributes
static const String	param_decoy_string_

static const String	param_minborder_

static const String	param_maxborder_

static const String	param_mindeltas_

static const String	param_minionsmatched_

static const String	param_uniquexl_

static const String	param_no_qvalues_

static const String	param_minscore_

static const String	param_binsize_

static const String	crosslink_class_intradecoys_

static const String	crosslink_class_fulldecoysintralinks_

static const String	crosslink_class_interdecoys_

static const String	crosslink_class_fulldecoysinterlinks_

static const String	crosslink_class_monodecoys_

static const String	crosslink_class_intralinks_

static const String	crosslink_class_interlinks_

static const String	crosslink_class_monolinks_

static const String	crosslink_class_decoys_

static const String	crosslink_class_targets_

static const String	crosslink_class_hybriddecoysintralinks_

static const String	crosslink_class_hybriddecoysinterlinks_

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 Member Functions inherited from DefaultParamHandler
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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Calculates false discovery rate estimates on crosslink identifications.

This tool calculates and FDR estimate for crosslink identifications, which are produced by OpenPepXL. The method employed currently is identical to the target-decoy approach used by xProphet (Walzthoeni et al., 2012). Consequently, this tool can also consume xquest.xml files (produced either by OpenPepXL or xQuest). The tool supports output in the idXML and mzIdentML formats.

Experimental classes:: This tool is work in progress and usage and input requirements might change.

Member Enumeration Documentation

◆ ExitCodes

enum ExitCodes

Exit codes.

Enumerator
EXECUTION_OK
ILLEGAL_PARAMETERS
UNEXPECTED_RESULT

Constructor & Destructor Documentation

◆ XFDRAlgorithm()

XFDRAlgorithm ( )

Default constructor.

◆ ~XFDRAlgorithm()

~XFDRAlgorithm ( )

override

Default destructor.

Member Function Documentation

◆ assignTypes_()

static void assignTypes_	(	PeptideHit &	pep_id,
		StringList &	types
	)

staticprivate

Inspects a PeptideIdentification and assigns all cross-link types that this identification belongs to.

Parameters

pep_id	Peptide ID to be assigned.
types	Result vector containing the names of the crosslink classes

◆ calc_qfdr_()

static void calc_qfdr_	(	const std::vector< double > &	fdr,
		std::vector< double > &	qfdr
	)

staticprivate

Calculates the qFDR values for the provided FDR values, assuming that the FDRs are sorted by score in the input vector.

Parameters

fdr	Vector with FDR values which should be used for qFDR calculation
qfdr	Result qFDR values

◆ fdr_xprophet_()

void fdr_xprophet_	(	std::map< String, Math::Histogram<> > &	cum_histograms,
		const String &	targetclass,
		const String &	decoyclass,
		const String &	fulldecoyclass,
		std::vector< double > &	fdr,
		bool	mono
	)		const

private

xprophet method for target hits counting as implemented in xProphet

Target counting as performed by the xProphet software package

Parameters

	cum_histograms	Cumulative score distributions
	targetclass	Name of key for targets in `cum_histograms`
	decoyclass	Name of key for decoys in `cum_histograms`
	fulldecoyclass	Name of key for full decoys in `cum_histograms`
[out]	fdr	Output FDR values
	mono

◆ findTopUniqueHits_()

void findTopUniqueHits_ ( std::vector< PeptideIdentification > & peptide_ids )

private

◆ getId_()

String getId_ ( const PeptideHit & ph ) const

private

◆ getMinIonsMatched_()

static Size getMinIonsMatched_ ( const PeptideHit & ph )

inlinestaticprivate

References MetaInfoInterface::getMetaValue().

◆ initDataStructures_()

void initDataStructures_	(	std::vector< PeptideIdentification > &	peptide_ids,
		ProteinIdentification &	protein_id
	)

private

Prepares vector of PeptideIdentification such that it can be processed downstream. The encompassed steps are:

Set min_score_ and max_score_ encountered in the data
Ensure that crosslink_type and crosslink_rank are available in the PeptideIdentification
Define the crosslink as either inter/or intraprotein
Set the identifier of the Peptide Identification if there is only one protein identification

◆ isSameProtein_()

static bool isSameProtein_	(	String	prot1,
		String	prot2,
		const String &	decoy_string
	)

inlinestaticprivate

Determines whether the Peptide Evidences belong to the same protein, modulo decoy.

References String::hasSubstring(), and String::substitute().

◆ run()

ExitCodes run	(	std::vector< PeptideIdentification > &	peptide_ids,
		ProteinIdentification &	protein_id
	)

Performs the main function of this class, the FDR estimation for cross-linked peptide experiments.

Parameters

peptide_ids	The PeptideIdentifications from an XL-MS experiment
protein_id	The ProteinIdentification from an XL-MS experiment

◆ setInterProtein_()

static void setInterProtein_	(	PeptideHit &	ph,
		const bool	value
	)

inlinestaticprivate

References MetaInfoInterface::setMetaValue().

◆ setIntraProtein_()

static void setIntraProtein_	(	PeptideHit &	ph,
		const bool	value
	)

inlinestaticprivate

References MetaInfoInterface::setMetaValue().

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

◆ validateClassArguments()

ExitCodes validateClassArguments ( ) const

Checks whether the parameters of the object are valid.

Returns: ExitCode EXECUTION_OK if they are valid, ILLEGAL_PARAMETERS otherwise

◆ writeArgumentsLog_()

void writeArgumentsLog_ ( ) const

private

Member Data Documentation

◆ arg_binsize_

double arg_binsize_

private

◆ arg_maxborder_

double arg_maxborder_

private

◆ arg_minborder_

double arg_minborder_

private

◆ arg_mindeltas_

double arg_mindeltas_

private

◆ arg_minionsmatched_

Int arg_minionsmatched_

private

◆ arg_minscore_

double arg_minscore_

private

◆ arg_no_qvalues_

bool arg_no_qvalues_

private

◆ arg_uniquex_

bool arg_uniquex_

private

◆ cross_link_classes_

std::map<String, std::vector<String> > cross_link_classes_

private

◆ crosslink_class_decoys_

const String crosslink_class_decoys_

staticprivate

◆ crosslink_class_fulldecoysinterlinks_

const String crosslink_class_fulldecoysinterlinks_

staticprivate

◆ crosslink_class_fulldecoysintralinks_

const String crosslink_class_fulldecoysintralinks_

staticprivate

◆ crosslink_class_hybriddecoysinterlinks_

const String crosslink_class_hybriddecoysinterlinks_

staticprivate

◆ crosslink_class_hybriddecoysintralinks_

const String crosslink_class_hybriddecoysintralinks_

staticprivate

◆ crosslink_class_interdecoys_

const String crosslink_class_interdecoys_

staticprivate

◆ crosslink_class_interlinks_

const String crosslink_class_interlinks_

staticprivate

◆ crosslink_class_intradecoys_

const String crosslink_class_intradecoys_

staticprivate

◆ crosslink_class_intralinks_

const String crosslink_class_intralinks_

staticprivate

◆ crosslink_class_monodecoys_

const String crosslink_class_monodecoys_

staticprivate

◆ crosslink_class_monolinks_

const String crosslink_class_monolinks_

staticprivate

◆ crosslink_class_targets_

const String crosslink_class_targets_

staticprivate

◆ decoy_string_

String decoy_string_

private

◆ max_score_

Int max_score_

private

◆ min_score_

Int min_score_

private

◆ param_binsize_

const String param_binsize_

staticprivate

◆ param_decoy_string_

const String param_decoy_string_

staticprivate

◆ param_maxborder_

const String param_maxborder_

staticprivate

◆ param_minborder_

const String param_minborder_

staticprivate

◆ param_mindeltas_

const String param_mindeltas_

staticprivate

◆ param_minionsmatched_

const String param_minionsmatched_

staticprivate

◆ param_minscore_

const String param_minscore_

staticprivate

◆ param_no_qvalues_

const String param_no_qvalues_

staticprivate

◆ param_uniquexl_

const String param_uniquexl_

staticprivate

◆ unique_id_scores_

std::vector<double> unique_id_scores_

private

◆ unique_ids_

std::vector<String> unique_ids_

private

Public Types

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ExitCodes

Constructor & Destructor Documentation

◆ XFDRAlgorithm()

◆ ~XFDRAlgorithm()

Member Function Documentation

◆ assignTypes_()

◆ calc_qfdr_()

◆ fdr_xprophet_()

◆ findTopUniqueHits_()

◆ getId_()

◆ getMinIonsMatched_()

◆ initDataStructures_()

◆ isSameProtein_()

◆ run()

◆ setInterProtein_()

◆ setIntraProtein_()

◆ updateMembers_()

◆ validateClassArguments()

◆ writeArgumentsLog_()

Member Data Documentation

◆ arg_binsize_

◆ arg_maxborder_

◆ arg_minborder_

◆ arg_mindeltas_

◆ arg_minionsmatched_

◆ arg_minscore_

◆ arg_no_qvalues_

◆ arg_uniquex_

◆ cross_link_classes_

◆ crosslink_class_decoys_

◆ crosslink_class_fulldecoysinterlinks_

◆ crosslink_class_fulldecoysintralinks_

◆ crosslink_class_hybriddecoysinterlinks_

◆ crosslink_class_hybriddecoysintralinks_

◆ crosslink_class_interdecoys_

◆ crosslink_class_interlinks_

◆ crosslink_class_intradecoys_

◆ crosslink_class_intralinks_

◆ crosslink_class_monodecoys_

◆ crosslink_class_monolinks_

◆ crosslink_class_targets_

◆ decoy_string_

◆ max_score_

◆ min_score_

◆ param_binsize_

◆ param_decoy_string_

◆ param_maxborder_

◆ param_minborder_

◆ param_mindeltas_

◆ param_minionsmatched_

◆ param_minscore_

◆ param_no_qvalues_

◆ param_uniquexl_

◆ unique_id_scores_

◆ unique_ids_