| OpenMS 2.5.0

Public Member Functions | Protected Types | Protected Member Functions | List of all members
ElutionModelFitter Class Reference

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...
| ~ElutionModelFitter () override
| 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 &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 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: 0.0 | 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 | 1.0 | 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
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

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)

## ◆ 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