#include <OpenMS/ANALYSIS/OPENSWATH/ConfidenceScoring.h>

Inheritance diagram for ConfidenceScoring:

Collaboration diagram for ConfidenceScoring:

Classes
struct	GLM_
	Binomial GLM. More...

struct	RTNorm_
	Helper for RT normalization (range 0-100) More...

Public Member Functions
	ConfidenceScoring (bool test_mode_=false)
	Constructor. More...

virtual	~ConfidenceScoring ()

void	initialize (const TargetedExperiment &library, const Size n_decoys, const Size n_transitions, const TransformationDescription &rt_trafo)

void	initializeGlm (double intercept, double rt_coef, double int_coef)

void	scoreMap (FeatureMap &features)
	Score a feature map -> make sure the class is properly initialized. More...

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

	~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...

Protected Types
typedef boost::bimap< double, boost::bimaps::multiset_of< double > >	BimapType
	Mapping: Q3 m/z <-> transition intensity (maybe not unique!) More...

Protected Member Functions
void	chooseDecoys_ ()
	Randomize the list of decoy indexes. More...

double	manhattanDist_ (DoubleList x, DoubleList y)
	Manhattan distance. More...

double	getAssayRT_ (const TargetedExperiment::Peptide &assay)
	Get the retention time of an assay. More...

void	extractIntensities_ (BimapType &intensity_map, Size n_transitions, DoubleList &intensities)

double	scoreAssay_ (const TargetedExperiment::Peptide &assay, double feature_rt, DoubleList &feature_intensities, const std::set< String > &transition_ids=std::set< String >())

void	scoreFeature_ (Feature &feature)
	Score a feature. More...

Protected Attributes
struct OpenMS::ConfidenceScoring::GLM_	glm_

struct OpenMS::ConfidenceScoring::RTNorm_	rt_norm_

TargetedExperiment	library_
	assay library More...

IntList	decoy_index_
	indexes of assays to use as decoys More...

Size	n_decoys_
	number of decoys to use (per feature/true assay) More...

Map< String, IntList >	transition_map_
	assay (ID) -> transitions (indexes) More...

Size	n_transitions_
	number of transitions to consider More...

TransformationDescription	rt_trafo_
	RT transformation to map measured RTs to assay RTs. More...

boost::mt19937	generator_
	random number generation engine More...

boost::variate_generator< boost::mt19937 &, boost::uniform_int<> >	rand_gen_
	Random number generator (must be initialized in init. list of c'tor!) More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

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

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Member Typedef Documentation

◆ BimapType

typedef boost::bimap<double, boost::bimaps::multiset_of<double> > BimapType

protected

Mapping: Q3 m/z <-> transition intensity (maybe not unique!)

Constructor & Destructor Documentation

◆ ConfidenceScoring()

ConfidenceScoring ( bool test_mode_ = false )

inlineexplicit

Constructor.

◆ ~ConfidenceScoring()

virtual ~ConfidenceScoring ( )

inlinevirtual

Member Function Documentation

◆ chooseDecoys_()

void chooseDecoys_ ( )

protected

Randomize the list of decoy indexes.

◆ extractIntensities_()

void extractIntensities_	(	BimapType &	intensity_map,
		Size	n_transitions,
		DoubleList &	intensities
	)

protected

Extract the n_transitions highest intensities from intensity_map, store them in intensities

◆ getAssayRT_()

double getAssayRT_ ( const TargetedExperiment::Peptide & assay )

protected

Get the retention time of an assay.

◆ initialize()

void initialize	(	const TargetedExperiment &	library,
		const Size	n_decoys,
		const Size	n_transitions,
		const TransformationDescription &	rt_trafo
	)

inline

◆ initializeGlm()

void initializeGlm	(	double	intercept,
		double	rt_coef,
		double	int_coef
	)

inline

◆ manhattanDist_()

double manhattanDist_	(	DoubleList	x,
		DoubleList	y
	)

protected

Manhattan distance.

◆ scoreAssay_()

double scoreAssay_	(	const TargetedExperiment::Peptide &	assay,
		double	feature_rt,
		DoubleList &	feature_intensities,
		const std::set< String > &	transition_ids = `std::set< String >()`
	)

protected

Score the assay assay against feature data (feature_rt, feature_intensities), optionally using only the specified transitions (transition_ids)

◆ scoreFeature_()

void scoreFeature_ ( Feature & feature )

protected

Score a feature.

◆ scoreMap()

void scoreMap ( FeatureMap & features )

inline

Score a feature map -> make sure the class is properly initialized.

both functions initializeGlm and initialize need to be called first.

The input to the program is

a transition library which contains peptides with corresponding assays.
a feature map where each feature corresponds to an assay (mapped with MetaValue "PeptideRef") and each feature has as many subordinates as the assay has transitions (mapped with MetaValue "native_id").

References TargetedExperiment::getPeptides(), TargetedExperiment::getTransitions(), UniqueIdInterface::getUniqueId(), OPENMS_LOG_DEBUG, and OPENMS_LOG_WARN.

Member Data Documentation

◆ decoy_index_

IntList decoy_index_

protected

indexes of assays to use as decoys

◆ generator_

boost::mt19937 generator_

protected

random number generation engine

◆ glm_

struct OpenMS::ConfidenceScoring::GLM_ glm_

protected

◆ library_

TargetedExperiment library_

protected

assay library

◆ n_decoys_

Size n_decoys_

protected

number of decoys to use (per feature/true assay)

◆ n_transitions_

Size n_transitions_

protected

number of transitions to consider

◆ rand_gen_

boost::variate_generator<boost::mt19937&, boost::uniform_int<> > rand_gen_

protected

Random number generator (must be initialized in init. list of c'tor!)

◆ rt_norm_

struct OpenMS::ConfidenceScoring::RTNorm_ rt_norm_

protected

◆ rt_trafo_

TransformationDescription rt_trafo_

protected

RT transformation to map measured RTs to assay RTs.

◆ transition_map_

Map<String, IntList> transition_map_

protected

assay (ID) -> transitions (indexes)

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BimapType

Constructor & Destructor Documentation

◆ ConfidenceScoring()

◆ ~ConfidenceScoring()

Member Function Documentation

◆ chooseDecoys_()

◆ extractIntensities_()

◆ getAssayRT_()

◆ initialize()

◆ initializeGlm()

◆ manhattanDist_()

◆ scoreAssay_()

◆ scoreFeature_()

◆ scoreMap()

Member Data Documentation

◆ decoy_index_

◆ generator_

◆ glm_

◆ library_

◆ n_decoys_

◆ n_transitions_

◆ rand_gen_

◆ rt_norm_

◆ rt_trafo_

◆ transition_map_