The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria. More...

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

Inheritance diagram for MRMFeatureFilter:

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Collaboration diagram for MRMFeatureFilter:

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

	~MRMFeatureFilter () override
	Destructor. More...

void	getDefaultParameters (Param &params) const
	Get the class' default parameters. More...

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

void	FilterFeatureMap (FeatureMap &features, const MRMFeatureQC &filter_criteria, const TargetedExperiment &transitions)
	Flags or filters features and subordinates in a FeatureMap. More...

void	FilterFeatureMapPercRSD (FeatureMap &features, const MRMFeatureQC &filter_criteria, const MRMFeatureQC &filter_values)
	Flags or filters features and subordinates in a FeatureMap based on a user defined set of filter values derived from calling `EstimatePercRSD`. The user supplied filter_criteria represents the bounds on acceptable PercentRSD values. NOTE that flagging nor filtering will be done on the labels and transitions type counts. More...

void	FilterFeatureMapBackgroundInterference (FeatureMap &features, const MRMFeatureQC &filter_criteria, const MRMFeatureQC &filter_values)
	Flags or filters features and subordinates in a FeatureMap based on a user defined set of filter values derived from calling `EstimateBackgroundInterferences`. The user supplied filter_criteria represents the bounds on acceptable PercentBackgroundInterference values. NOTE that filtering is only done on the `Intensity` member. More...

void	EstimateDefaultMRMFeatureQCValues (const std::vector< FeatureMap > &samples, MRMFeatureQC &filter_template, const TargetedExperiment &transitions, const bool &init_template_values) const
	Estimate the lower and upper bound values for the MRMFeatureQC class based on a user supplied template. The template can either be initialized from the first sample (meaning all initial template values are over written) or not (meaning the initial template values will be updated if the ranges are found to be too narrow) More...

void	TransferLLOQAndULOQToCalculatedConcentrationBounds (const std::vector< AbsoluteQuantitationMethod > &quantitation_method, MRMFeatureQC &filter_template)
	Transfer the lower and upper bound values for the calculated concentrations based off of the AbsoluteQuantitationMethod. More...

void	EstimatePercRSD (const std::vector< FeatureMap > &samples, MRMFeatureQC &filter_template, const TargetedExperiment &transitions) const
	Estimate the feature variability as measured by PercentRSD from multiple pooled QC samples or replicate Unknown samples. The returned filter_template can then be used by `FilterFeatureMapPercRSD` in order to filter based on the PercentRSD user defined limits. More...

void	EstimateBackgroundInterferences (const std::vector< FeatureMap > &samples, MRMFeatureQC &filter_template, const TargetedExperiment &transitions) const
	Estimate the background interference level based on the average values from Blank samples. The returned filter_template can then be used by `FilterFeatureMapBackgroundInterference` in order to filter on the `Intensity` members of MRMFeatureQC::ComponentGroupQCs and MRMFeatureQC::ComponentQCs. More...

double	calculateIonRatio (const Feature &component_1, const Feature &component_2, const String &feature_name) const
	Calculates the ion ratio between two transitions. More...

double	calculateRTDifference (Feature &component_1, Feature &component_2) const
	Calculates the retention time difference between two features. More...

double	calculateResolution (Feature &component_1, Feature &component_2) const
	Calculates the resolution between two features. More...

bool	checkMetaValue (const Feature &component, const String &meta_value_key, const double &meta_value_l, const double &meta_value_u, bool &key_exists) const
	Checks if the metaValue is within the user specified range. More...

void	updateMetaValue (const Feature &component, const String &meta_value_key, double &meta_value_l, double &meta_value_u, bool &key_exists) const
	Updates the metaValue ranges based on the value given. More...

void	setMetaValue (const Feature &component, const String &meta_value_key, double &meta_value_l, double &meta_value_u, bool &key_exists) const
	Uses the supplied value to set the metaValue ranges. More...

void	initMetaValue (const Feature &component, const String &meta_value_key, double &meta_value_l, double &meta_value_u, bool &key_exists) const
	Uses the supplied value to initialize the metaValue ranges to the same value. More...

std::map< String, int >	countLabelsAndTransitionTypes (const Feature &component_group, const TargetedExperiment &transitions) const
	Count the number of heavy/light labels and quantifying/detecting/identifying transitions. More...

StringList	getUniqueSorted (const StringList &messages) const
	Sorts the messages and returns a copy without duplicates. More...

void	accumulateFilterValues (std::vector< MRMFeatureQC > &filter_values, const std::vector< FeatureMap > &samples, const MRMFeatureQC &filter_template, const TargetedExperiment &transitions) const
	Accumulate feature values from a list of FeatureMaps. More...

void	zeroFilterValues (MRMFeatureQC &filter_zeros, const MRMFeatureQC &filter_template) const
	Set all members in MRMFeatureQC to zero. More...

void	calculateFilterValuesMean (MRMFeatureQC &filter_mean, const std::vector< MRMFeatureQC > &filter_values, const MRMFeatureQC &filter_template) const
	Calculate the mean of each MRMFeatureQC parameter from a list of MRMFeatureQC classes. More...

void	calculateFilterValuesVar (MRMFeatureQC &filter_var, const std::vector< MRMFeatureQC > &filter_values, const MRMFeatureQC &filter_mean, const MRMFeatureQC &filter_template) const
	Calculate the var of each MRMFeatureQC parameter from a list of MRMFeatureQC classes. More...

void	calculateFilterValuesPercRSD (MRMFeatureQC &filter_rsd, const MRMFeatureQC &filter_mean, const MRMFeatureQC &filter_var) const
	Calculate the relative standard deviation (PercentRSD) of each MRMFeatureQC parameter from pre-computed mean and variance values. More...

template<typename T >
bool	checkRange (const T &value, const T &value_l, const T &value_u) const
	Checks that the range of value is bracketed by value_l and value_u. More...

template<typename T >
void	updateRange (const T &value, T &value_l, T &value_u) const
	Updates value_l and value_u according to whether value is greater than value_u or less than value_l. More...

template<typename T >
void	setRange (const T &value, T &value_l, T &value_u) const
	Sets value_l and value_u to bracket the range 0 to value or value to 0 depending on if value is >0. More...

template<typename T >
void	initRange (const T &value, T &value_l, T &value_u) const
	Sets value_l and value_u to value. 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...

Private Attributes
String	flag_or_filter_
	flag or filter (i.e., remove) features that do not pass the QC 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...

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

Detailed Description

The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
flag_or_filter	string	flag	flag, filter	Flag or Filter (i.e., remove) Components or transitions that do not pass the QC.

Note:

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

Constructor & Destructor Documentation

◆ MRMFeatureFilter()

MRMFeatureFilter ( )

Constructor.

◆ ~MRMFeatureFilter()

~MRMFeatureFilter ( )

override

Destructor.

Member Function Documentation

◆ accumulateFilterValues()

void accumulateFilterValues	(	std::vector< MRMFeatureQC > &	filter_values,
		const std::vector< FeatureMap > &	samples,
		const MRMFeatureQC &	filter_template,
		const TargetedExperiment &	transitions
	)		const

Accumulate feature values from a list of FeatureMaps.

Parameters

[out]	filter_values	A list of MRMFeatureQC objects filled with the values determined by the filter_template from the samples
[in]	samples	A list of feature maps
[in]	filter_template	A MRMFeatureQC object that will be used as a template to fill in values derived from the sample feature maps
[in]	transitions	transitions from a TargetedExperiment

◆ calculateFilterValuesMean()

void calculateFilterValuesMean	(	MRMFeatureQC &	filter_mean,
		const std::vector< MRMFeatureQC > &	filter_values,
		const MRMFeatureQC &	filter_template
	)		const

Calculate the mean of each MRMFeatureQC parameter from a list of MRMFeatureQC classes.

Parameters

[out]	filter_mean	A MRMFeatureQC object whose members will be replaced by the mean values
[in]	filter_values	A list of MRMFeatureQC objects
[in]	filter_template	A MRMFeatureQC object that will be used as a template to fill in values

◆ calculateFilterValuesPercRSD()

void calculateFilterValuesPercRSD	(	MRMFeatureQC &	filter_rsd,
		const MRMFeatureQC &	filter_mean,
		const MRMFeatureQC &	filter_var
	)		const

Calculate the relative standard deviation (PercentRSD) of each MRMFeatureQC parameter from pre-computed mean and variance values.

Parameters

[out]	filter_rsd	A MRMFeatureQC object whose members will be replaced by PercentRSD
[in]	filter_var	A MRMFeatureQC object with the variance
[in]	filter_mean	A MRMFeatureQC object with the mean

◆ calculateFilterValuesVar()

void calculateFilterValuesVar	(	MRMFeatureQC &	filter_var,
		const std::vector< MRMFeatureQC > &	filter_values,
		const MRMFeatureQC &	filter_mean,
		const MRMFeatureQC &	filter_template
	)		const

Calculate the var of each MRMFeatureQC parameter from a list of MRMFeatureQC classes.

Parameters

[out]	filter_var	A MRMFeatureQC object whose members will be replaced by the variance of the values
[in]	filter_values	A list of MRMFeatureQC objects
[in]	filter_mean	A MRMFeatureQC object with the mean values of the filter_values
[in]	filter_template	A MRMFeatureQC object that will be used as a template to fill in values

◆ calculateIonRatio()

double calculateIonRatio	(	const Feature &	component_1,
		const Feature &	component_2,
		const String &	feature_name
	)		const

Calculates the ion ratio between two transitions.

Parameters

component_1	component of the numerator
component_2	component of the denominator
feature_name	name of the feature to calculate the ratio on e.g., peak_apex, peak_area

Returns: The ratio.

◆ calculateResolution()

double calculateResolution	(	Feature &	component_1,
		Feature &	component_2
	)		const

Calculates the resolution between two features.

Parameters

component_1	component 1
component_2	component 2

Returns: The difference.

◆ calculateRTDifference()

double calculateRTDifference	(	Feature &	component_1,
		Feature &	component_2
	)		const

Calculates the retention time difference between two features.

Parameters

component_1	First eluting component
component_2	Second eluting component

Returns: The difference.

◆ checkMetaValue()

bool checkMetaValue	(	const Feature &	component,
		const String &	meta_value_key,
		const double &	meta_value_l,
		const double &	meta_value_u,
		bool &	key_exists
	)		const

Checks if the metaValue is within the user specified range.

Parameters

[in]	component	component of the numerator
[in]	meta_value_key	Name of the metaValue
[in]	meta_value_l	Lower bound (inclusive) for the metaValue range
[in]	meta_value_u	Upper bound (inclusive) for the metaValue range
[out]	key_exists	true if the given key is found, false otherwise

Returns: True if the metaValue is within the bounds, and False otherwise.

◆ checkRange()

bool checkRange	(	const T &	value,
		const T &	value_l,
		const T &	value_u
	)		const

Checks that the range of value is bracketed by value_l and value_u.

◆ countLabelsAndTransitionTypes()

std::map<String,int> countLabelsAndTransitionTypes	(	const Feature &	component_group,
		const TargetedExperiment &	transitions
	)		const

Count the number of heavy/light labels and quantifying/detecting/identifying transitions.

Parameters

component_group	Component group with subordinates
transitions	Transitions from a TargetedExperiment

Returns: Map of labels/transition types and their corresponding number.

◆ EstimateBackgroundInterferences()

void EstimateBackgroundInterferences	(	const std::vector< FeatureMap > &	samples,
		MRMFeatureQC &	filter_template,
		const TargetedExperiment &	transitions
	)		const

Estimate the background interference level based on the average values from Blank samples. The returned filter_template can then be used by FilterFeatureMapBackgroundInterference in order to filter on the Intensity members of MRMFeatureQC::ComponentGroupQCs and MRMFeatureQC::ComponentQCs.

Parameters

[in]	samples	multiple Blank samples to estimate the background intensity values FeatureMaps
[in,out]	filter_template	A MRMFeatureQC class that will be used as a template to determine what FeatureMap values to estimate the PercentInterference. The average values will be stored in the upper bound parameter of the filter_template
[in]	transitions	transitions from a TargetedExperiment

◆ EstimateDefaultMRMFeatureQCValues()

void EstimateDefaultMRMFeatureQCValues	(	const std::vector< FeatureMap > &	samples,
		MRMFeatureQC &	filter_template,
		const TargetedExperiment &	transitions,
		const bool &	init_template_values
	)		const

Estimate the lower and upper bound values for the MRMFeatureQC class based on a user supplied template. The template can either be initialized from the first sample (meaning all initial template values are over written) or not (meaning the initial template values will be updated if the ranges are found to be too narrow)

Parameters

[in]	samples	Samples (typically Standards) from which to estimate the lower and upper bound values for the MRMFeatureQC members
[in,out]	filter_template	A MRMFeatureQC class that will be used as a template to fill in the estimated lower and upper values. A "template" is needed so that the MRMFeatureQC::meta_value_qc parameters that the FeatureMap::MetaValues that user would like estimated are known.
[in]	transitions	transitions from a TargetedExperiment
[in]	init_template_values	Boolean indicating whether to initialize the template values based on the first sample

◆ EstimatePercRSD()

void EstimatePercRSD	(	const std::vector< FeatureMap > &	samples,
		MRMFeatureQC &	filter_template,
		const TargetedExperiment &	transitions
	)		const

Estimate the feature variability as measured by PercentRSD from multiple pooled QC samples or replicate Unknown samples. The returned filter_template can then be used by FilterFeatureMapPercRSD in order to filter based on the PercentRSD user defined limits.

Parameters

[in]	samples	multiple pooled QC samples or replicate Unknown samples FeatureMaps
[in,out]	filter_template	A MRMFeatureQC class that will be used as a template to determine what FeatureMap values to estimate the PercentRSD for. The PercentRSD values will be stored in the upper bound parameter of the filter_template
[in]	transitions	transitions from a TargetedExperiment

◆ FilterFeatureMap()

void FilterFeatureMap	(	FeatureMap &	features,
		const MRMFeatureQC &	filter_criteria,
		const TargetedExperiment &	transitions
	)

Flags or filters features and subordinates in a FeatureMap.

Parameters

features	FeatureMap to flag or filter
filter_criteria	MRMFeatureQC class defining QC parameters
transitions	transitions from a TargetedExperiment

◆ FilterFeatureMapBackgroundInterference()

void FilterFeatureMapBackgroundInterference	(	FeatureMap &	features,
		const MRMFeatureQC &	filter_criteria,
		const MRMFeatureQC &	filter_values
	)

Flags or filters features and subordinates in a FeatureMap based on a user defined set of filter values derived from calling EstimateBackgroundInterferences. The user supplied filter_criteria represents the bounds on acceptable PercentBackgroundInterference values. NOTE that filtering is only done on the Intensity member.

Parameters

features	FeatureMap to flag or filter
filter_criteria	MRMFeatureQC class defining QC parameters defining the acceptable limits of PercentBackgroundInterference where PercentBackgroundInterference = (value Sample)/(value Blank)*100Percent
filter_values	MRMFeatureQC class filled with bounds representing the average values found in e.g., pooled QC samples or replicate Unknown samples

◆ FilterFeatureMapPercRSD()

void FilterFeatureMapPercRSD	(	FeatureMap &	features,
		const MRMFeatureQC &	filter_criteria,
		const MRMFeatureQC &	filter_values
	)

Flags or filters features and subordinates in a FeatureMap based on a user defined set of filter values derived from calling EstimatePercRSD. The user supplied filter_criteria represents the bounds on acceptable PercentRSD values. NOTE that flagging nor filtering will be done on the labels and transitions type counts.

Parameters

features	FeatureMap to flag or filter
filter_criteria	MRMFeatureQC class defining QC parameters defining the acceptable limits of the PercentRSD where PercentRSD = (value std dev)/(value mean)*100Percent
filter_values	MRMFeatureQC class filled with bounds representing the PercentRSD found in e.g., pooled QC samples or replicate Unknown samples

◆ getDefaultParameters()

void getDefaultParameters ( Param & params ) const

Get the class' default parameters.

Parameters

[out] params Output parameters

◆ getUniqueSorted()

StringList getUniqueSorted ( const StringList & messages ) const

Sorts the messages and returns a copy without duplicates.

Parameters

[in] messages A StringList containing the failure messages

Returns: A copy of the input, without duplicates

◆ initMetaValue()

void initMetaValue	(	const Feature &	component,
		const String &	meta_value_key,
		double &	meta_value_l,
		double &	meta_value_u,
		bool &	key_exists
	)		const

Uses the supplied value to initialize the metaValue ranges to the same value.

Parameters

[in]	component	component of the numerator
[in]	meta_value_key	Name of the metaValue
[in,out]	meta_value_l	Lower bound (inclusive) for the metaValue range
[in,out]	meta_value_u	Upper bound (inclusive) for the metaValue range
[out]	key_exists	true if the given key is found, false otherwise

◆ initRange()

void initRange	(	const T &	value,
		T &	value_l,
		T &	value_u
	)		const

Sets value_l and value_u to value.

◆ setMetaValue()

void setMetaValue	(	const Feature &	component,
		const String &	meta_value_key,
		double &	meta_value_l,
		double &	meta_value_u,
		bool &	key_exists
	)		const

Uses the supplied value to set the metaValue ranges.

Parameters

[in]	component	component of the numerator
[in]	meta_value_key	Name of the metaValue
[in,out]	meta_value_l	Lower bound (inclusive) for the metaValue range
[in,out]	meta_value_u	Upper bound (inclusive) for the metaValue range
[out]	key_exists	true if the given key is found, false otherwise

◆ setRange()

void setRange	(	const T &	value,
		T &	value_l,
		T &	value_u
	)		const

Sets value_l and value_u to bracket the range 0 to value or value to 0 depending on if value is >0.

◆ TransferLLOQAndULOQToCalculatedConcentrationBounds()

void TransferLLOQAndULOQToCalculatedConcentrationBounds	(	const std::vector< AbsoluteQuantitationMethod > &	quantitation_method,
		MRMFeatureQC &	filter_template
	)

Transfer the lower and upper bound values for the calculated concentrations based off of the AbsoluteQuantitationMethod.

Parameters

[in]	quantitation_method	The absolute quantitation methods that has been determined for each component
[in,out]	filter_template	A MRMFeatureQC class that will be used as a template to fill in the MRMFeatureQC::ComponentQCs.calculated_concentration bounds based on the LLOQ and ULOQ values given in the quantitation_method.

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

◆ updateMetaValue()

void updateMetaValue	(	const Feature &	component,
		const String &	meta_value_key,
		double &	meta_value_l,
		double &	meta_value_u,
		bool &	key_exists
	)		const

Updates the metaValue ranges based on the value given.

Parameters

[in]	component	component of the numerator
[in]	meta_value_key	Name of the metaValue
[in,out]	meta_value_l	Lower bound (inclusive) for the metaValue range
[in,out]	meta_value_u	Upper bound (inclusive) for the metaValue range
[out]	key_exists	true if the given key is found, false otherwise

◆ updateRange()

void updateRange	(	const T &	value,
		T &	value_l,
		T &	value_u
	)		const

Updates value_l and value_u according to whether value is greater than value_u or less than value_l.

◆ zeroFilterValues()

void zeroFilterValues	(	MRMFeatureQC &	filter_zeros,
		const MRMFeatureQC &	filter_template
	)		const

Set all members in MRMFeatureQC to zero.

Parameters

[out]	filter_zeros	A MRMFeatureQC object whose members have been set to 0
[in]	filter_template	A MRMFeatureQC object that will be used as a template to fill in values

Member Data Documentation

◆ flag_or_filter_

String flag_or_filter_

private

flag or filter (i.e., remove) features that do not pass the QC

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MRMFeatureFilter()

◆ ~MRMFeatureFilter()

Member Function Documentation

◆ accumulateFilterValues()

◆ calculateFilterValuesMean()

◆ calculateFilterValuesPercRSD()

◆ calculateFilterValuesVar()

◆ calculateIonRatio()

◆ calculateResolution()

◆ calculateRTDifference()

◆ checkMetaValue()

◆ checkRange()

◆ countLabelsAndTransitionTypes()

◆ EstimateBackgroundInterferences()

◆ EstimateDefaultMRMFeatureQCValues()

◆ EstimatePercRSD()

◆ FilterFeatureMap()

◆ FilterFeatureMapBackgroundInterference()

◆ FilterFeatureMapPercRSD()

◆ getDefaultParameters()

◆ getUniqueSorted()

◆ initMetaValue()

◆ initRange()

◆ setMetaValue()

◆ setRange()

◆ TransferLLOQAndULOQToCalculatedConcentrationBounds()

◆ updateMembers_()

◆ updateMetaValue()

◆ updateRange()

◆ zeroFilterValues()

Member Data Documentation

◆ flag_or_filter_