An algorithm to decharge small molecule features (i.e. as found by FeatureFinder). More...

#include <OpenMS/ANALYSIS/DECHARGING/MetaboliteFeatureDeconvolution.h>

Inheritance diagram for MetaboliteFeatureDeconvolution:

Collaboration diagram for MetaboliteFeatureDeconvolution:

Public Types
enum	CHARGEMODE { QFROMFEATURE = 1 , QHEURISTIC , QALL }

typedef DPosition< 2 >	ClusterPointType

typedef Feature::CoordinateType	CoordinateType

typedef ILPDCWrapper::PairsType	PairsType

Constructors and Destructor s
MassExplainer::AdductsType	potential_adducts_
	List of adducts used to explain mass differences. More...

std::map< Size, String >	map_label_
	labeling table More...

std::map< String, Size >	map_label_inverse_
	labeling table inverse More...

bool	enable_intensity_filter_
	status of intensity filter for edges More...

bool	negative_mode_
	status of ionization mode More...

CHARGEMODE	q_try_
	status of charge discovery More...

Int	verbose_level_
	amount of debug information displayed More...

	MetaboliteFeatureDeconvolution ()
	default constructor More...

	MetaboliteFeatureDeconvolution (const MetaboliteFeatureDeconvolution &source)
	Copy constructor. More...

MetaboliteFeatureDeconvolution &	operator= (const MetaboliteFeatureDeconvolution &source)
	Assignment operator. More...

	~MetaboliteFeatureDeconvolution () override
	destructor More...

void	compute (const FeatureMap &fm_in, FeatureMap &fm_out, ConsensusMap &cons_map, ConsensusMap &cons_map_p)
	Compute a zero-charge feature map from a set of charged features. More...

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

void	checkSolution_ (const ConsensusMap &cons_map) const

void	inferMoreEdges_ (PairsType &edges, std::map< Size, std::set< CmpInfo_ >> &feature_adducts)

void	candidateEdges_ (FeatureMap &fm_out, const Adduct &default_adduct, PairsType &feature_relation, std::map< Size, std::set< CmpInfo_ >> &feature_adducts)

void	annotate_feature_ (FeatureMap &fm_out, Adduct &default_adduct, Compomer &c, const Size f_idx, const UInt side, const Int new_q, const Int old_q)

void	printEdgesOfConnectedFeatures_ (Size idx_1, Size idx_2, const PairsType &feature_relation)
	A function mostly for debugging. More...

bool	intensityFilterPassed_ (const Int q1, const Int q2, const Compomer &cmp, const Feature &f1, const Feature &f2) const
	returns true if the intensity filter was passed or switched off More...

bool	chargeTestworthy_ (const Int feature_charge, const Int putative_charge, const bool other_unchanged) const
	determines if we should test a putative feature charge More...

Additional Inherited Members
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...

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

An algorithm to decharge small molecule features (i.e. as found by FeatureFinder).

Parameters of this class are:

Name	Type	Default	Restrictions	Description
charge_min	int	1		Minimal possible charge
charge_max	int	3		Maximal possible charge
charge_span_max	int	3	min: 1	Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge
q_try	string	feature	feature, heuristic, all	Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature').
retention_max_diff	float	1.0		Maximum allowed RT difference between any two features if their relation shall be determined
retention_max_diff_local	float	1.0		Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)
mass_max_diff	float	0.05	min: 0.0	Maximum allowed mass tolerance per feature. Defines a symmetric tolerance window around the feature. When looking at possible feature pairs, the allowed feature-wise errors are combined for consideration of possible adduct shifts. For ppm tolerances, each window is based on the respective observed feature mz (instead of putative experimental mzs causing the observed one)!
unit	string	Da	Da, ppm	Unit of the 'max_difference' parameter
potential_adducts	string list	[H:+:0.4, Na:+:0.25, NH4:+:0.25, K:+:0.1, H-2O-1:0:0.05]		Adducts used to explain mass differences in format: 'Elements:Charge(+/-/0):Probability[:RTShift[:Label]]', i.e. the number of '+' or '-' indicate the charge ('0' if neutral adduct), e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. The optional RTShift param indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:0:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As fifth parameter you can add a label for every feature with this adduct. This also determines the map number in the consensus file. Adduct element losses are written in the form 'H-2'. All provided adducts need to have the same charge sign or be neutral! Mixing of adducts with different charge directions is only allowed as neutral complexes. For example, 'H-1Na:0:0.05' can be used to model Sodium gains (with balancing deprotonation) in negative mode.
max_neutrals	int	1		Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!
use_minority_bound	string	true	true, false	Prune the considered adduct transitions by transition probabilities.
max_minority_bound	int	3	min: 0	Limits allowed adduct compositions and changes between compositions in the underlying graph optimization problem by introducing a probability-based threshold: the minority bound sets the maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant with maximum charge only containing the most likely adduct otherwise. E.g., for 'charge_max' 4 and 'max_minority_bound' 2 with most probable adduct being H+ and least probable adduct being Na+, this will allow adduct compositions of '2(H+),2(Na+)' but not of '1(H+),3(Na+)'. Further, adduct compositions/changes less likely than '2(H+),2(Na+)' will be discarded as well.
min_rt_overlap	float	0.66	min: 0.0 max: 1.0	Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)
intensity_filter	string	false	true, false	Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge.
negative_mode	string	false	true, false	Enable negative ionization mode.
default_map_label	string	decharged features		Label of map in output consensus file where all features are put by default
verbose_level	int	0	min: 0 max: 3	Amount of debug information given during processing.

Note:

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

Member Typedef Documentation

◆ ClusterPointType

typedef DPosition<2> ClusterPointType

◆ CoordinateType

typedef Feature::CoordinateType CoordinateType

◆ PairsType

typedef ILPDCWrapper::PairsType PairsType

Member Enumeration Documentation

◆ CHARGEMODE

enum CHARGEMODE

Enumerator
QFROMFEATURE
QHEURISTIC
QALL

Constructor & Destructor Documentation

◆ MetaboliteFeatureDeconvolution() [1/2]

MetaboliteFeatureDeconvolution ( )

default constructor

◆ MetaboliteFeatureDeconvolution() [2/2]

MetaboliteFeatureDeconvolution ( const MetaboliteFeatureDeconvolution & source )

Copy constructor.

◆ ~MetaboliteFeatureDeconvolution()

~MetaboliteFeatureDeconvolution ( )

override

destructor

Member Function Documentation

◆ annotate_feature_()

void annotate_feature_	(	FeatureMap &	fm_out,
		Adduct &	default_adduct,
		Compomer &	c,
		const Size	f_idx,
		const UInt	side,
		const Int	new_q,
		const Int	old_q
	)

protected

◆ candidateEdges_()

void candidateEdges_	(	FeatureMap &	fm_out,
		const Adduct &	default_adduct,
		PairsType &	feature_relation,
		std::map< Size, std::set< CmpInfo_ >> &	feature_adducts
	)

protected

◆ chargeTestworthy_()

bool chargeTestworthy_	(	const Int	feature_charge,
		const Int	putative_charge,
		const bool	other_unchanged
	)		const

protected

determines if we should test a putative feature charge

Answer query given the internal status of q_try. Features with q<=0 always return true.

◆ checkSolution_()

void checkSolution_ ( const ConsensusMap & cons_map ) const

protected

◆ compute()

void compute	(	const FeatureMap &	fm_in,
		FeatureMap &	fm_out,
		ConsensusMap &	cons_map,
		ConsensusMap &	cons_map_p
	)

Compute a zero-charge feature map from a set of charged features.

Find putative ChargePairs, then score them and hand over to ILP.

Parameters

fm_in	Input feature-map
fm_out	Output feature-map (sorted by position and augmented with user params)
cons_map	[out] Output of grouped features belonging to a charge group
cons_map_p	[out] Output of paired features connected by an edge

◆ inferMoreEdges_()

void inferMoreEdges_	(	PairsType &	edges,
		std::map< Size, std::set< CmpInfo_ >> &	feature_adducts
	)

protected

test if "simple" edges have alternative (more difficult explanation) supported by neighboring edges e.g. (.) -> (H+) might be augmented to (Na+) -> (H+Na+)

◆ intensityFilterPassed_()

bool intensityFilterPassed_	(	const Int	q1,
		const Int	q2,
		const Compomer &	cmp,
		const Feature &	f1,
		const Feature &	f2
	)		const

inlineprotected

returns true if the intensity filter was passed or switched off

Filter for adding an edge only when the two features connected by it, fulfill the intensity criterion.

◆ operator=()

MetaboliteFeatureDeconvolution& operator= ( const MetaboliteFeatureDeconvolution & source )

Assignment operator.

◆ printEdgesOfConnectedFeatures_()

void printEdgesOfConnectedFeatures_	(	Size	idx_1,
		Size	idx_2,
		const PairsType &	feature_relation
	)

protected

A function mostly for debugging.

◆ 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

◆ enable_intensity_filter_

bool enable_intensity_filter_

protected

status of intensity filter for edges

◆ map_label_

std::map<Size, String> map_label_

protected

labeling table

◆ map_label_inverse_

std::map<String, Size> map_label_inverse_

protected

labeling table inverse

◆ negative_mode_

bool negative_mode_

protected

status of ionization mode

◆ potential_adducts_

MassExplainer::AdductsType potential_adducts_

protected

List of adducts used to explain mass differences.

◆ q_try_

CHARGEMODE q_try_

protected

status of charge discovery

◆ verbose_level_

Int verbose_level_

protected

amount of debug information displayed

Public Types

Constructors and Destructor s

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ClusterPointType

◆ CoordinateType

◆ PairsType

Member Enumeration Documentation

◆ CHARGEMODE

Constructor & Destructor Documentation

◆ MetaboliteFeatureDeconvolution() [1/2]

◆ MetaboliteFeatureDeconvolution() [2/2]

◆ ~MetaboliteFeatureDeconvolution()

Member Function Documentation

◆ annotate_feature_()

◆ candidateEdges_()

◆ chargeTestworthy_()

◆ checkSolution_()

◆ compute()

◆ inferMoreEdges_()

◆ intensityFilterPassed_()

◆ operator=()

◆ printEdgesOfConnectedFeatures_()

◆ updateMembers_()

Member Data Documentation

◆ enable_intensity_filter_

◆ map_label_

◆ map_label_inverse_

◆ negative_mode_

◆ potential_adducts_

◆ q_try_

◆ verbose_level_