The PeakPickerMRM finds peaks a single chromatogram. More...

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

Inheritance diagram for PeakPickerMRM:

Collaboration diagram for PeakPickerMRM:

Public Types
enum	FLOATINDICES { IDX_FWHM = 0 , IDX_ABUNDANCE = 1 , IDX_LEFTBORDER = 2 , IDX_RIGHTBORDER = 3 , SIZE_OF_FLOATINDICES }
	indices into FloatDataArrays of resulting picked chromatograms More...

Public Member Functions
	PeakPickerMRM ()
	Constructor. More...

	~PeakPickerMRM () override
	Destructor. More...

void	pickChromatogram (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom)
	Finds peaks in a single chromatogram and annotates left/right borders. More...

void	pickChromatogram (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom, MSChromatogram &smoothed_chrom)
	Finds peaks in a single chromatogram and annotates left/right borders. 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...

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...

Protected Member Functions
void	pickChromatogramCrawdad_ (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom)

void	pickChromatogram_ (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom)

void	integratePeaks_ (const MSChromatogram &chromatogram)
	Compute peak area (peak integration) More...

Size	findClosestPeak_ (const MSChromatogram &chromatogram, double target_rt, Size current_peak=0)
	Helper function to find the closest peak in a chromatogram to "target_rt". More...

void	removeOverlappingPeaks_ (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom)
	Helper function to remove overlapping peaks in a single Chromatogram. More...

void	updateMembers_ () override
	Synchronize members with param class. More...

PeakPickerMRM &	operator= (const PeakPickerMRM &rhs)
	Assignment operator is protected for algorithm. More...

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

Protected Attributes
UInt	sgolay_frame_length_
	Frame length for the SGolay smoothing. More...

UInt	sgolay_polynomial_order_
	Polynomial order for the SGolay smoothing. More...

double	gauss_width_
	Width of the Gaussian smoothing. More...

bool	use_gauss_
	Whether to use Gaussian smoothing. More...

bool	remove_overlapping_
	Whether to resolve overlapping peaks. More...

double	peak_width_
	Forced peak with. More...

double	signal_to_noise_
	Signal to noise threshold. More...

double	sn_win_len_
	Signal to noise window length. More...

UInt	sn_bin_count_
	Signal to noise bin count. More...

bool	write_sn_log_messages_
	Whether to write out log messages of the SN estimator. More...

String	method_
	Peak picker method. More...

std::vector< double >	integrated_intensities_
	Temporary vector to hold the integrated intensities. More...

std::vector< int >	left_width_
	Temporary vector to hold the peak left widths. More...

std::vector< int >	right_width_
	Temporary vector to hold the peak right widths. More...

PeakPickerHiRes	pp_

SavitzkyGolayFilter	sgolay_

GaussFilter	gauss_

SignalToNoiseEstimatorMedian< MSChromatogram >	snt_

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...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Detailed Description

The PeakPickerMRM finds peaks a single chromatogram.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
sgolay_frame_length	int	15		The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.
sgolay_polynomial_order	int	3		Order of the polynomial that is fitted.
gauss_width	float	50.0		Gaussian width in seconds, estimated peak size.
use_gauss	string	true	false, true	Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
peak_width	float	-1.0		Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.
signal_to_noise	float	1.0	min: 0.0	Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.
sn_win_len	float	1000.0		Signal to noise window length.
sn_bin_count	int	30		Signal to noise bin count.
write_sn_log_messages	string	false	true, false	Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
remove_overlapping_peaks	string	false	false, true	Try to remove overlapping peaks during peak picking
method	string	corrected	legacy, corrected, crawdad	Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).

Note:

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

It uses the PeakPickerHiRes internally to find interesting seed candidates. These candidates are then expanded and a right/left border of the peak is searched. Additionally, overlapping peaks can be removed.

Member Enumeration Documentation

◆ FLOATINDICES

enum FLOATINDICES

indices into FloatDataArrays of resulting picked chromatograms

Enumerator
IDX_FWHM
IDX_ABUNDANCE
IDX_LEFTBORDER
IDX_RIGHTBORDER
SIZE_OF_FLOATINDICES

Constructor & Destructor Documentation

◆ PeakPickerMRM()

PeakPickerMRM ( )

Constructor.

◆ ~PeakPickerMRM()

~PeakPickerMRM ( )

inlineoverride

Destructor.

Member Function Documentation

◆ findClosestPeak_()

Size findClosestPeak_	(	const MSChromatogram &	chromatogram,
		double	target_rt,
		Size	current_peak = `0`
	)

protected

Helper function to find the closest peak in a chromatogram to "target_rt".

The search will start from the index current_peak, so the function is assuming the closest peak is to the right of current_peak.

It will return the index of the closest peak in the chromatogram.

◆ integratePeaks_()

void integratePeaks_ ( const MSChromatogram & chromatogram )

protected

Compute peak area (peak integration)

◆ operator=()

PeakPickerMRM& operator= ( const PeakPickerMRM & rhs )

protected

Assignment operator is protected for algorithm.

◆ pickChromatogram() [1/2]

void pickChromatogram	(	const MSChromatogram &	chromatogram,
		MSChromatogram &	picked_chrom
	)

Finds peaks in a single chromatogram and annotates left/right borders.

It uses a modified algorithm of the PeakPickerHiRes

This function will return a picked chromatogram

◆ pickChromatogram() [2/2]

void pickChromatogram	(	const MSChromatogram &	chromatogram,
		MSChromatogram &	picked_chrom,
		MSChromatogram &	smoothed_chrom
	)

Finds peaks in a single chromatogram and annotates left/right borders.

It uses a modified algorithm of the PeakPickerHiRes

This function will return a picked chromatogram and a smoothed chromatogram

◆ pickChromatogram_()

void pickChromatogram_	(	const MSChromatogram &	chromatogram,
		MSChromatogram &	picked_chrom
	)

protected

◆ pickChromatogramCrawdad_()

void pickChromatogramCrawdad_	(	const MSChromatogram &	chromatogram,
		MSChromatogram &	picked_chrom
	)

protected

◆ removeOverlappingPeaks_()

void removeOverlappingPeaks_	(	const MSChromatogram &	chromatogram,
		MSChromatogram &	picked_chrom
	)

protected

Helper function to remove overlapping peaks in a single Chromatogram.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ gauss_

GaussFilter gauss_

protected

◆ gauss_width_

double gauss_width_

protected

Width of the Gaussian smoothing.

◆ integrated_intensities_

std::vector<double> integrated_intensities_

protected

Temporary vector to hold the integrated intensities.

◆ left_width_

std::vector<int> left_width_

protected

Temporary vector to hold the peak left widths.

◆ method_

String method_

protected

Peak picker method.

◆ peak_width_

double peak_width_

protected

Forced peak with.

◆ pp_

PeakPickerHiRes pp_

protected

◆ remove_overlapping_

bool remove_overlapping_

protected

Whether to resolve overlapping peaks.

◆ right_width_

std::vector<int> right_width_

protected

Temporary vector to hold the peak right widths.

◆ sgolay_

SavitzkyGolayFilter sgolay_

protected

◆ sgolay_frame_length_

UInt sgolay_frame_length_

protected

Frame length for the SGolay smoothing.

◆ sgolay_polynomial_order_

UInt sgolay_polynomial_order_

protected

Polynomial order for the SGolay smoothing.

◆ signal_to_noise_

double signal_to_noise_

protected

Signal to noise threshold.

◆ sn_bin_count_

UInt sn_bin_count_

protected

Signal to noise bin count.

◆ sn_win_len_

double sn_win_len_

protected

Signal to noise window length.

◆ snt_

SignalToNoiseEstimatorMedian<MSChromatogram > snt_

protected

◆ use_gauss_

bool use_gauss_

protected

Whether to use Gaussian smoothing.

◆ write_sn_log_messages_

bool write_sn_log_messages_

protected

Whether to write out log messages of the SN estimator.

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ FLOATINDICES

Constructor & Destructor Documentation

◆ PeakPickerMRM()

◆ ~PeakPickerMRM()

Member Function Documentation

◆ findClosestPeak_()

◆ integratePeaks_()

◆ operator=()

◆ pickChromatogram() [1/2]

◆ pickChromatogram() [2/2]

◆ pickChromatogram_()

◆ pickChromatogramCrawdad_()

◆ removeOverlappingPeaks_()

◆ updateMembers_()

Member Data Documentation

◆ gauss_

◆ gauss_width_

◆ integrated_intensities_

◆ left_width_

◆ method_

◆ peak_width_

◆ pp_

◆ remove_overlapping_

◆ right_width_

◆ sgolay_

◆ sgolay_frame_length_

◆ sgolay_polynomial_order_

◆ signal_to_noise_

◆ sn_bin_count_

◆ sn_win_len_

◆ snt_

◆ use_gauss_

◆ write_sn_log_messages_