Correlates individual masstraces found in mass spectrometric maps. More...

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

Inheritance diagram for MasstraceCorrelator:

Collaboration diagram for MasstraceCorrelator:

Public Types
typedef std::vector< std::pair< double, double > >	MasstracePointsType

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

Public Member Functions
	MasstraceCorrelator ()

	~MasstraceCorrelator () override

void	createPseudoSpectra (const ConsensusMap &map, MSExperiment &pseudo_spectra, Size min_peak_nr, double min_correlation, int max_lag, double max_rt_apex_difference)

void	scoreHullpoints (const MasstracePointsType &hull_points1, const MasstracePointsType &hull_points2, int &lag, double &lag_intensity, double &pearson_score, const double min_corr, const int max_lag, const double mindiff=0.1)

void	createConsensusMapCache (const ConsensusMap &map, std::vector< MasstracePointsType > &feature_points, std::vector< std::pair< double, double > > &max_intensities, std::vector< double > &rt_cache)

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...

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...

Protected Member Functions
void	matchMassTraces_ (const MasstracePointsType &hull_points1, const MasstracePointsType &hull_points2, std::vector< double > &vec1, std::vector< double > &vec2, double mindiff, double padEnds=true)
	Match up two mass traces with potentially missing values. More...

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...

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...

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

Correlates individual masstraces found in mass spectrometric maps.

The MasstraceCorrelator offers several functions to correlate individual mass traces using the normalized Cross-Correlation and pearson scoring of the OpenSWATH module.

Member Typedef Documentation

◆ MasstracePointsType

typedef std::vector<std::pair<double, double> > MasstracePointsType

Constructor & Destructor Documentation

◆ MasstraceCorrelator()

MasstraceCorrelator ( )

◆ ~MasstraceCorrelator()

~MasstraceCorrelator ( )

override

Member Function Documentation

◆ createConsensusMapCache()

void createConsensusMapCache	(	const ConsensusMap &	map,
		std::vector< MasstracePointsType > &	feature_points,
		std::vector< std::pair< double, double > > &	max_intensities,
		std::vector< double > &	rt_cache
	)

◆ createPseudoSpectra()

void createPseudoSpectra	(	const ConsensusMap &	map,
		MSExperiment &	pseudo_spectra,
		Size	min_peak_nr,
		double	min_correlation,
		int	max_lag,
		double	max_rt_apex_difference
	)

Compute pseudo-spectra from a set of (MS2) masstraces

This function will take a set of masstraces (consensus map) as input and produce a vector of pseudo spectra as output (pseudo_spectra result vector).

It basically makes an all-vs-all comparison of all masstraces against each other and scores them on how similar they are in their mass traces.

This assumes that the consensus feature is only from one (SWATH) map This assumes that the consensus map is sorted by intensity

◆ matchMassTraces_()

void matchMassTraces_	(	const MasstracePointsType &	hull_points1,
		const MasstracePointsType &	hull_points2,
		std::vector< double > &	vec1,
		std::vector< double > &	vec2,
		double	mindiff,
		double	padEnds = `true`
	)

protected

Match up two mass traces with potentially missing values.

To compute correlations on masstraces, they need to have the same length and matching points. This function matches two masstraces by RT and identifies points that are the same in retention time (see mindiff parameter) and matches them. If no match is found, a missing value is assumed and they are filled with zeros. Thus, if the two retention times are less than mindiff apart, the two entries are considered to be equal, otherwise one is assumed to be zero).

This is useful for matching mass traces that are not of the exact same length and/or have missing values.

Parameters

hull_points1	The first input mass trace
hull_points2	The second input mass trace
vec1	The intensities of the first mass trace with matched-up points
vec2	The intensities of the second mass trace with matched-up points
mindiff	The minimal difference in RT for points to match up
padEnds	Whether to pad ends with zeros

◆ scoreHullpoints()

void scoreHullpoints	(	const MasstracePointsType &	hull_points1,
		const MasstracePointsType &	hull_points2,
		int &	lag,
		double &	lag_intensity,
		double &	pearson_score,
		const double	min_corr,
		const int	max_lag,
		const double	mindiff = `0.1`
	)

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members