PipEchoAlgorithm Class Reference

Match-between-runs feature grouping via the PIP-ECHO algorithm. More...

#include <OpenMS/ANALYSIS/MAPMATCHING/PipEchoAlgorithm.h>

Inheritance diagram for PipEchoAlgorithm:

Collaboration diagram for PipEchoAlgorithm:

Public Member Functions
	PipEchoAlgorithm ()
	Constructor.
	PipEchoAlgorithm (PipEchoAlgorithm &&)=delete
PipEchoAlgorithm &	operator= (PipEchoAlgorithm &&)=delete
	PipEchoAlgorithm (const PipEchoAlgorithm &other)=delete
	Copy constructor.
PipEchoAlgorithm &	operator= (const PipEchoAlgorithm &source)=delete
	Assignment operator.
	~PipEchoAlgorithm () override
	Destructor.
void	group (const std::vector< FeatureMap > &features, ConsensusMap &consensus) override
	Groups corresponding features across the feature maps of one fraction.
Public Member Functions inherited from FeatureGroupingAlgorithm
	FeatureGroupingAlgorithm ()
	Default constructor.
	~FeatureGroupingAlgorithm () override
	Destructor.
virtual void	group (const std::vector< ConsensusMap > &maps, ConsensusMap &out)
void	transferSubelements (const std::vector< ConsensusMap > &maps, ConsensusMap &out) const
	Transfers subelements (grouped features) from input consensus maps to the result consensus map.
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.

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 Member Functions inherited from FeatureGroupingAlgorithm
template<class MapType >
void	postprocess_ (const std::vector< MapType > &maps, ConsensusMap &out)
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.
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

Match-between-runs feature grouping via the PIP-ECHO algorithm.

Groups features that represent the same identified peptide across multiple retention-time-aligned LC-MS runs of a single fraction. Identifications are transferred to runs in which a feature was detected but not identified (match-between-runs); candidate transfers are scored and filtered at a controlled false-discovery rate using a target/decoy model.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
fdr	float	0.05	min: 0.0 max: 1.0	MBR FDR threshold (0.05=5%).
random_seed	int	0		Seed for the random number generator used to select decoy donors. A fixed seed makes results reproducible.
min_decoys	int	20	min: 1	Minimum number of MBR decoy transfers required before any transferred feature is kept. Transferred features are also dropped whenever the requested 'fdr' cannot be resolved by the available decoys (1/decoys > fdr). When transfers are dropped, only direct identifications are retained. A 'fdr' of 1.0 disables FDR control and keeps all transfers regardless of this value.
max_training_points	int	50000	min: 0	Upper bound on the number of candidate transfers used to TRAIN the transfer-FDR SVM in each cross-validation fold (0 = unlimited). Predictions and the FDR/q-values are always computed over ALL transfers, so this only bounds the SVM-fitting cost and does not change which transfers are scored. Runs with very many features per run can otherwise make the SVM grid search slow. When the cap is hit, a deterministic stratified subsample is used: both labelled classes (decoys and positives) are kept whole if they fit, otherwise the minority class is kept whole and the majority is score-spread sampled to fit the budget.
distance_RT:max_difference	float	100.0	min: 0.0	Never pair features with a larger RT distance (in seconds).
distance_MZ:max_difference	float	10.0	min: 0.0	Never pair features with larger m/z distance (unit defined by 'unit')
distance_MZ:unit	string	ppm	Da, ppm	Unit of the 'max_difference' parameter

Note:

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

Constructor & Destructor Documentation

PipEchoAlgorithm() [1/3]

PipEchoAlgorithm

(

)

Constructor.

PipEchoAlgorithm() [2/3]

PipEchoAlgorithm ( PipEchoAlgorithm &&  )

delete

PipEchoAlgorithm() [3/3]

PipEchoAlgorithm ( const PipEchoAlgorithm &  other )

delete

Copy constructor.

~PipEchoAlgorithm()

~PipEchoAlgorithm ( )

override

Destructor.

Member Function Documentation

group()

void group ( const std::vector< FeatureMap > &  features, ConsensusMap &  consensus  )

overridevirtual

Groups corresponding features across the feature maps of one fraction.

Features representing the same identified peptide are grouped together and, where possible, identifications are transferred between runs.

Parameters

features	The input feature maps (same fraction) to link.
consensus	The resulting consensus map of grouped features.

Precondition

The input maps must be retention-time aligned (e.g. via a map-alignment algorithm) and originate from the same fraction.

Implements FeatureGroupingAlgorithm.

operator=() [1/2]

PipEchoAlgorithm & operator= ( const PipEchoAlgorithm &  source )

delete

Assignment operator.

operator=() [2/2]

PipEchoAlgorithm & operator= ( PipEchoAlgorithm &&  )

delete