Simulates peptide detectability. More...
#include <OpenMS/SIMULATION/DetectabilitySimulation.h>
Public Member Functions | |
| DetectabilitySimulation & | operator= (const DetectabilitySimulation &source) |
| Assignment operator. | |
| void | filterDetectability (FeatureMapSim &features) |
| Filters the given peptide features for detectibility. | |
| void | predictDetectabilities (std::vector< String > &peptides_vector, std::vector< DoubleReal > &labels, std::vector< DoubleReal > &detectabilities) |
Constructors and Destructors | |
| DetectabilitySimulation () | |
| Constructor taking a random generator. | |
| DetectabilitySimulation (const DetectabilitySimulation &source) | |
| Copy constructor. | |
| virtual | ~DetectabilitySimulation () |
| Destructor. | |
Protected Member Functions | |
| void | svmFilter_ (FeatureMapSim &) |
| Filter the feature map using a svm model. | |
| void | noFilter_ (FeatureMapSim &) |
| Do not filter the feature map, just set the detectability to a default value. | |
Private Member Functions | |
| void | setDefaultParams_ () |
| Set default parameters. | |
| void | updateMembers_ () |
| Synchronize members with param class. | |
Private Attributes | |
| DoubleReal | min_detect_ |
| Minimum allowed detectability likelihood of a peptide. | |
| OpenMS::String | dt_model_file_ |
| Name of the svm model file. | |
Detailed Description
Simulates peptide detectability.
The peptide detectability is predicted based on a support-vector machine. Alternativly the detectability can be set to a default value for all peptides if no model is given.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| dt_simulation_on | string | false | true, false | Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count |
| min_detect | float | 0.5 | Minimum peptide detectability accepted. Peptides with a lower score will be removed | |
| dt_model_file | string | examples/simulation/DTPredict.model | SVM model for peptide detectability prediction |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
Constructor taking a random generator.
| DetectabilitySimulation | ( | const DetectabilitySimulation & | source | ) |
Copy constructor.
| virtual ~DetectabilitySimulation | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| void filterDetectability | ( | FeatureMapSim & | features | ) |
Filters the given peptide features for detectibility.
Based on the provided method (SVM or simple) all peptide features are removed that do not have a sufficient peptide detectibility.
- Parameters:
-
features Feature map that will be filtered for detectibility
| void noFilter_ | ( | FeatureMapSim & | ) | [protected] |
Do not filter the feature map, just set the detectability to a default value.
| DetectabilitySimulation& operator= | ( | const DetectabilitySimulation & | source | ) |
Assignment operator.
| void predictDetectabilities | ( | std::vector< String > & | peptides_vector, | |
| std::vector< DoubleReal > & | labels, | |||
| std::vector< DoubleReal > & | detectabilities | |||
| ) |
| void setDefaultParams_ | ( | ) | [private] |
Set default parameters.
| void svmFilter_ | ( | FeatureMapSim & | ) | [protected] |
Filter the feature map using a svm model.
| void updateMembers_ | ( | ) | [private, virtual] |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
Member Data Documentation
OpenMS::String dt_model_file_ [private] |
Name of the svm model file.
DoubleReal min_detect_ [private] |
Minimum allowed detectability likelihood of a peptide.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |