ElutionModelFitter Class Reference

Helper class for fitting elution models to features. More...

#include <OpenMS/FEATUREFINDER/ElutionModelFitter.h>

Inheritance diagram for ElutionModelFitter:

Collaboration diagram for ElutionModelFitter:

Public Member Functions
	ElutionModelFitter ()
	Default constructor.
	~ElutionModelFitter () override
	Destructor.
void	fitElutionModels (FeatureMap &features)
	Fit models of elution profiles to all features (and validate them)
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Protected Types
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace	MassTrace
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces	MassTraces

Protected Member Functions
double	calculateFitQuality_ (const TraceFitter *fitter, const MassTraces &traces)
	Calculate quality of model fit (mean relative error)
void	fitAndValidateModel_ (TraceFitter *fitter, MassTraces &traces, Feature &feature, double region_start, double region_end, bool asymmetric, double area_limit, double check_boundaries)
	Helper function to fit (and validate) a model for one set of mass traces.
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.
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

Helper class for fitting elution models to features.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
asymmetric	string	false	true, false	Fit an asymmetric (exponential-Gaussian hybrid) model? By default a symmetric (Gaussian) model is used.
add_zeros	float	0.2	min: 0.0	Add zero-intensity points outside the feature range to constrain the model fit. This parameter sets the weight given to these points during model fitting; '0' to disable.
unweighted_fit	string	false	true, false	Suppress weighting of mass traces according to theoretical intensities when fitting elution models
no_imputation	string	false	true, false	If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate
each_trace	string	false	true, false	Fit elution model to each individual mass trace
check:min_area	float	1.0	min: 0.0	Lower bound for the area under the curve of a valid elution model
check:boundaries	float	0.5	min: 0.0 max: 1.0	Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting
check:width	float	10.0	min: 0.0	Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace').
check:asymmetry	float	10.0	min: 0.0	Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace').

Note:

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

Member Typedef Documentation

MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace

protected

MassTraces

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces

protected

Constructor & Destructor Documentation

ElutionModelFitter()

ElutionModelFitter

(

)

Default constructor.

~ElutionModelFitter()

~ElutionModelFitter ( )

override

Destructor.

Member Function Documentation

calculateFitQuality_()

double calculateFitQuality_ ( const TraceFitter *  fitter, const MassTraces &  traces  )

protected

Calculate quality of model fit (mean relative error)

fitAndValidateModel_()

void fitAndValidateModel_ ( TraceFitter *  fitter, MassTraces &  traces, Feature &  feature, double  region_start, double  region_end, bool  asymmetric, double  area_limit, double  check_boundaries  )

protected

Helper function to fit (and validate) a model for one set of mass traces.

fitElutionModels()

void fitElutionModels

(

FeatureMap &

features

)

Fit models of elution profiles to all features (and validate them)

Assumptions (not checked!):

• all features have meta values "left-"/"rightWidth" giving RT start/end
• all features have subordinates (for the mass traces/transitions)
• each subordinate has an appropriate meta value "isotope_probability"
• each subordinate has one convex hull
• all convex hulls in one feature contain the same number (> 0) of points
• the y coordinates of the hull points store the intensities