Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental). More...

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

Inheritance diagram for BayesianProteinInferenceAlgorithm:

Collaboration diagram for BayesianProteinInferenceAlgorithm:

Public Member Functions
	BayesianProteinInferenceAlgorithm (unsigned int debug_lvl=0)
	Constructor. More...

	~BayesianProteinInferenceAlgorithm () override=default
	Destructor. More...

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

void	inferPosteriorProbabilities (std::vector< ProteinIdentification > &proteinIDs, std::vector< PeptideIdentification > &peptideIDs, bool greedy_group_resolution, std::optional< const ExperimentalDesign > exp_des=std::optional< const ExperimentalDesign >())
	Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function. Writes its results into protein and (optionally also) peptide hits (as new score). Optionally adds indistinguishable protein groups with separate scores, too. Output scores are always posterior probabilities. Input can be posterior or error probabilities. See Param object defaults_ within the BayesianProteinInferenceAlgorithm for more settings. Currently only takes first proteinID run and all peptides (irrespective of getIdentifier()). More...

void	inferPosteriorProbabilities (ConsensusMap &cmap, bool greedy_group_resolution, std::optional< const ExperimentalDesign > exp_des=std::optional< const ExperimentalDesign >())
	Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function. Writes its results into protein and (optionally also) peptide hits (as new score). Optionally adds indistinguishable protein groups with separate scores, too. Output scores are always posterior probabilities. Input can be posterior or error probabilities. See Param object defaults_ within the BayesianProteinInferenceAlgorithm for more settings. Currently only takes first proteinID run and all peptides (irrespective of getIdentifier()). 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	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 () const
	Ends the progress display. More...

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

Private Member Functions
void	inferPosteriorProbabilities_ (Internal::IDBoostGraph &ibg)

GridSearch< double, double, double >	initGridSearchFromParams_ (std::vector< double > &alpha_search, std::vector< double > &beta_search, std::vector< double > &gamma_search)
	read Param object and set the grid More...

void	setScoreTypeAndSettings_ (ProteinIdentification &proteinIDs)
	set score type and settings for every ProteinID run processed More...

void	resetProteinScores_ (ProteinIdentification &protein_id, bool keep_old_as_prior)
	reset all protein scores to 0.0, save old ones as Prior MetaValue if requested More...

Private Attributes
std::function< void(PeptideIdentification &)>	checkConvertAndFilterPepHits_

unsigned int	debug_lvl_

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

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...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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

Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimental).

Filters for best n PSMs per spectrum.
Calculates and filters for best peptide per spectrum.
Builds a k-partite graph from the structures.
Finds and splits into connected components by DFS
Extends the graph by adding layers from indist. protein groups, peptides with the same parents and optionally some additional layers (peptide sequence, charge, replicate -> extended model = experimental)
Builds a factor graph representation of a Bayesian network using the Evergreen library See model param section. It is based on the Fido noisy-OR model with an option for regularizing the number of proteins per peptide.
Performs loopy belief propagation on the graph and queries protein, protein group and/or peptide posteriors See loopy_belief_propagation param section.
Learns best parameters via grid search if the parameters were not given in the param section.
Writes posteriors to peptides and/or proteins and adds indistinguishable protein groups to the underlying data structures.
Can make use of OpenMP to parallelize over connected components.

Constructor & Destructor Documentation

◆ BayesianProteinInferenceAlgorithm()

BayesianProteinInferenceAlgorithm ( unsigned int debug_lvl = 0 )

explicit

Constructor.

Todo:: is there a better way to pass the debug level from TOPPBase?

◆ ~BayesianProteinInferenceAlgorithm()

~BayesianProteinInferenceAlgorithm ( )

overridedefault

Destructor.

Member Function Documentation

◆ inferPosteriorProbabilities() [1/2]

void inferPosteriorProbabilities	(	ConsensusMap &	cmap,
		bool	greedy_group_resolution,
		std::optional< const ExperimentalDesign >	exp_des = `std::optional< const ExperimentalDesign >()`
	)

Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function. Writes its results into protein and (optionally also) peptide hits (as new score). Optionally adds indistinguishable protein groups with separate scores, too. Output scores are always posterior probabilities. Input can be posterior or error probabilities. See Param object defaults_ within the BayesianProteinInferenceAlgorithm for more settings. Currently only takes first proteinID run and all peptides (irrespective of getIdentifier()).

Parameters

cmap	Features with input/output peptides and proteins (from getProteinIdentifications)
greedy_group_resolution	Do greedy group resolution? Remove all but best association for "razor" peptides.
exp_des	Experimental design can be used to create an extended graph with replicate information. (experimental)

◆ inferPosteriorProbabilities() [2/2]

void inferPosteriorProbabilities	(	std::vector< ProteinIdentification > &	proteinIDs,
		std::vector< PeptideIdentification > &	peptideIDs,
		bool	greedy_group_resolution,
		std::optional< const ExperimentalDesign >	exp_des = `std::optional< const ExperimentalDesign >()`
	)

Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function. Writes its results into protein and (optionally also) peptide hits (as new score). Optionally adds indistinguishable protein groups with separate scores, too. Output scores are always posterior probabilities. Input can be posterior or error probabilities. See Param object defaults_ within the BayesianProteinInferenceAlgorithm for more settings. Currently only takes first proteinID run and all peptides (irrespective of getIdentifier()).

Parameters

proteinIDs	Input/output proteins
peptideIDs	Input/output peptides
greedy_group_resolution	Do greedy group resolution? Remove all but best association for "razor" peptides.
exp_des	Experimental design can be used to create an extended graph with replicate information. (experimental)

Todo:: loop over all runs

◆ inferPosteriorProbabilities_()

void inferPosteriorProbabilities_ ( Internal::IDBoostGraph & ibg )

private

after a graph was built, use this method to perform inference and write results to the structures with which the graph was built

◆ initGridSearchFromParams_()

GridSearch<double,double,double> initGridSearchFromParams_	(	std::vector< double > &	alpha_search,
		std::vector< double > &	beta_search,
		std::vector< double > &	gamma_search
	)

private

read Param object and set the grid

◆ resetProteinScores_()

void resetProteinScores_	(	ProteinIdentification &	protein_id,
		bool	keep_old_as_prior
	)

private

reset all protein scores to 0.0, save old ones as Prior MetaValue if requested

◆ setScoreTypeAndSettings_()

void setScoreTypeAndSettings_ ( ProteinIdentification & proteinIDs )

private

set score type and settings for every ProteinID run processed

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

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.

Member Data Documentation

◆ checkConvertAndFilterPepHits_

std::function<void(PeptideIdentification&)> checkConvertAndFilterPepHits_

private

function initialized based on the algorithm parameters that is used to filter PeptideHits

Todo:: extend to allow filtering only for the current run

◆ debug_lvl_

unsigned int debug_lvl_

private

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BayesianProteinInferenceAlgorithm()

◆ ~BayesianProteinInferenceAlgorithm()

Member Function Documentation

◆ inferPosteriorProbabilities() [1/2]

◆ inferPosteriorProbabilities() [2/2]

◆ inferPosteriorProbabilities_()

◆ initGridSearchFromParams_()

◆ resetProteinScores_()

◆ setScoreTypeAndSettings_()

◆ updateMembers_()

Member Data Documentation

◆ checkConvertAndFilterPepHits_

◆ debug_lvl_