Helper class for fitting elution models to features. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/ElutionModelFitter.h>
Inheritance diagram for ElutionModelFitter:
Public Member Functions | |
| ElutionModelFitter () | |
| Default constructor. More... | |
| virtual | ~ElutionModelFitter () |
| Destructor. More... | |
| void | fitElutionModels (FeatureMap &features) |
| Fit models of elution profiles to all features (and validate them) 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 ¶m) |
| 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 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) More... | |
| 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. More... | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Additional Inherited Members | |
| 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
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 | 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 |
| check:min_area | float | 1 | min: 0 | Lower bound for the area under the curve of a valid elution model |
| check:boundaries | float | 0.5 | min: 0 max: 1 | 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 | min: 0 | Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable |
| check:asymmetry | float | 10 | min: 0 | Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Member Typedef Documentation
◆ MassTrace
|
protected |
◆ MassTraces
|
protected |
Constructor & Destructor Documentation
◆ ElutionModelFitter()
Default constructor.
◆ ~ElutionModelFitter()
|
virtual |
Destructor.
Member Function Documentation
◆ calculateFitQuality_()
|
protected |
Calculate quality of model fit (mean relative error)
◆ 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