Extracts chromatographic peaks from a mass trace. More...

#include <OpenMS/FEATUREFINDER/ElutionPeakDetection.h>

Inheritance diagram for ElutionPeakDetection:

Collaboration diagram for ElutionPeakDetection:

Public Member Functions
	ElutionPeakDetection ()
	Default Constructor. More...

	~ElutionPeakDetection () override
	Destructor. More...

void	detectPeaks (MassTrace &mt, std::vector< MassTrace > &single_mtraces)
	Extracts chromatographic peaks from a single MassTrace and stores the resulting split traces in a vector of new mass traces. More...

void	detectPeaks (std::vector< MassTrace > &mt_vec, std::vector< MassTrace > &single_mtraces)
	Extracts chromatographic peaks from multiple MassTraces and stores the resulting split traces in a vector of new mass traces. More...

void	filterByPeakWidth (std::vector< MassTrace > &, std::vector< MassTrace > &)
	Filter out mass traces below lower 5 % quartile and above upper 95 % quartile. More...

double	computeMassTraceNoise (const MassTrace &)
	Compute noise level (as RMSE of the actual signal and the smoothed signal) More...

double	computeMassTraceSNR (const MassTrace &)
	Compute the signal to noise ratio (estimated by computeMassTraceNoise) More...

double	computeApexSNR (const MassTrace &)
	Compute the signal to noise ratio at the apex (estimated by computeMassTraceNoise) More...

void	findLocalExtrema (const MassTrace &tr, const Size &num_neighboring_peaks, std::vector< Size > &chrom_maxes, std::vector< Size > &chrom_mins) const
	Computes local extrema on a mass trace. More...

void	smoothData (MassTrace &mt, int win_size) const
	adds smoothed_intensities to internal data of `mt` 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...

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

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Member Functions
void	detectElutionPeaks_ (MassTrace &, std::vector< MassTrace > &)
	Main function to do the work. More...

Private Attributes
double	chrom_fwhm_

double	chrom_peak_snr_

double	min_fwhm_

double	max_fwhm_

String	pw_filtering_
	Type of width filtering. More...

bool	mt_snr_filtering_
	Whether to apply S/N filtering. More...

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 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

Extracts chromatographic peaks from a mass trace.

Mass traces may consist of several consecutively (partly overlapping) eluting peaks, e.g., stemming from (almost) isobaric compounds that are separated by retention time. Especially in metabolomics, isomeric compounds with exactly the same mass but different retentional behaviour may still be contained in the same mass trace.

This method first applies smoothing on the mass trace's intensities, then detects local minima/maxima in order to separate the chromatographic peaks from each other. Detection of maxima is performed on the smoothed intensities and uses a fixed peak width (given as parameter chrom_fwhm) within which only a single maximum is expected. Currently smoothing is done using SavitzkyGolay smoothing with a second order polynomial and a frame length of the fixed peak width.

Depending on the "width_filtering" parameters, mass traces are filtered by length in seconds ("fixed" filter) or by quantile.

The output of the algorithm is a set of chromatographic peaks for each mass trace, i.e. a vector of split mass traces (see ElutionPeakDetection parameters).

In general, a user would want to call the "detectPeaks" functions, potentially followed by the "filterByPeakWidth" function.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
chrom_fwhm	float	5.0		Expected full-width-at-half-maximum of chromatographic peaks (in seconds).
chrom_peak_snr	float	3.0		Minimum signal-to-noise a mass trace should have.
width_filtering	string	fixed	off, fixed, auto	Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution.
min_fwhm	float	1.0		Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.
max_fwhm	float	60.0		Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.
masstrace_snr_filtering	string	false	true, false	Apply post-filtering by signal-to-noise ratio after smoothing.

Note:

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

Constructor & Destructor Documentation

◆ ElutionPeakDetection()

ElutionPeakDetection ( )

Default Constructor.

◆ ~ElutionPeakDetection()

~ElutionPeakDetection ( )

override

Destructor.

Member Function Documentation

◆ computeApexSNR()

double computeApexSNR ( const MassTrace & )

Compute the signal to noise ratio at the apex (estimated by computeMassTraceNoise)

◆ computeMassTraceNoise()

double computeMassTraceNoise ( const MassTrace & )

Compute noise level (as RMSE of the actual signal and the smoothed signal)

◆ computeMassTraceSNR()

double computeMassTraceSNR ( const MassTrace & )

Compute the signal to noise ratio (estimated by computeMassTraceNoise)

◆ detectElutionPeaks_()

void detectElutionPeaks_	(	MassTrace &	,
		std::vector< MassTrace > &
	)

private

Main function to do the work.

◆ detectPeaks() [1/2]

void detectPeaks	(	MassTrace &	mt,
		std::vector< MassTrace > &	single_mtraces
	)

Extracts chromatographic peaks from a single MassTrace and stores the resulting split traces in a vector of new mass traces.

Note: Smoothed intensities are added to mt_vec

Parameters

mt	Input mass trace
single_mtraces	Output single mass traces (detected peaks)

◆ detectPeaks() [2/2]

void detectPeaks	(	std::vector< MassTrace > &	mt_vec,
		std::vector< MassTrace > &	single_mtraces
	)

Extracts chromatographic peaks from multiple MassTraces and stores the resulting split traces in a vector of new mass traces.

Note: Smoothed intensities are added to mt_vec

Parameters

mt_vec	Input mass traces
single_mtraces	Output single mass traces (detected peaks)

◆ filterByPeakWidth()

void filterByPeakWidth	(	std::vector< MassTrace > &	,
		std::vector< MassTrace > &
	)

Filter out mass traces below lower 5 % quartile and above upper 95 % quartile.

◆ findLocalExtrema()

void findLocalExtrema	(	const MassTrace &	tr,
		const Size &	num_neighboring_peaks,
		std::vector< Size > &	chrom_maxes,
		std::vector< Size > &	chrom_mins
	)		const

Computes local extrema on a mass trace.

This function computes local extrema on a given input mass trace. It works on the smoothed intensities which must be available at this step. Initially it identifies potential maxima as peaks that have maximum intensity within a range of peak +/- num_neighboring_peaks. All such maxima in the smoothed data get added to the list of maxima. Minima are found through bisection between the maxima.

Parameters

tr	Input mass trace
num_neighboring_peaks	How many data points are expected to belong to a peak, i.e. the expected peak width (this is used to split traces and find maxima)
chrom_maxes	Output of maxima (gets cleared)
chrom_mins	Output of minima (gets cleared)

Returns a vector of indices where a maxima may occur (chrom_maxes) and a vector of indices where a minima may occur (chrom_mins).

Note: this expects that the input mass trace has been smoothed before and the smoothed intensities are available through tr.getSmoothedIntensities().

◆ smoothData()

void smoothData	(	MassTrace &	mt,
		int	win_size
	)		const

adds smoothed_intensities to internal data of mt

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

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

◆ chrom_fwhm_

double chrom_fwhm_

private

◆ chrom_peak_snr_

double chrom_peak_snr_

private

◆ max_fwhm_

double max_fwhm_

private

◆ min_fwhm_

double min_fwhm_

private

◆ mt_snr_filtering_

bool mt_snr_filtering_

private

Whether to apply S/N filtering.

◆ pw_filtering_

String pw_filtering_

private

Type of width filtering.

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ElutionPeakDetection()

◆ ~ElutionPeakDetection()

Member Function Documentation

◆ computeApexSNR()

◆ computeMassTraceNoise()

◆ computeMassTraceSNR()

◆ detectElutionPeaks_()

◆ detectPeaks() [1/2]

◆ detectPeaks() [2/2]

◆ filterByPeakWidth()

◆ findLocalExtrema()

◆ smoothData()

◆ updateMembers_()

Member Data Documentation

◆ chrom_fwhm_

◆ chrom_peak_snr_

◆ max_fwhm_

◆ min_fwhm_

◆ mt_snr_filtering_

◆ pw_filtering_