Implementation of a cross valdidation training for the PILIS model. More...
#include <OpenMS/ANALYSIS/ID/PILISCrossValidation.h>
Classes | |
| struct | Option |
| This struct represents a cross validation option. More... | |
| struct | Peptide |
| this struct represents a peptide spectrum pair More... | |
Public Member Functions | |
Constructors and destructors | |
| PILISCrossValidation () | |
| Default constructor. | |
| PILISCrossValidation (const PILISCrossValidation &rhs) | |
| copy constructor | |
| virtual | ~PILISCrossValidation () |
| desctructor | |
| PILISCrossValidation & | operator= (const PILISCrossValidation &rhs) |
| assignment operator | |
Accessors | |
| void | setOptions (const Map< String, Option > &rhs) |
| sets the options which should be used for the cross validation | |
| void | setOption (const String &name, const Option &option) |
| sets a option to be used for the cross validation | |
| void | apply (Param &PILIS_param, const PILISModel &base_model, const std::vector< Peptide > &peptides) |
| performs a cross validation and write optimized param into PILIS_param | |
| DoubleReal | scoreHits (const std::vector< std::vector< std::vector< RichPeakSpectrum > > > &sim_spectra, const std::vector< std::vector< RichPeakSpectrum > > &exp_spectra) |
| compares experimental and simulated spectra and returns a score | |
Protected Member Functions | |
| DoubleReal | scoreSpectra_ (const RichPeakSpectrum &spec1, const RichPeakSpectrum &spec2) |
| void | partition_ (std::vector< std::vector< Peptide > > &parts, const std::vector< Peptide > &source) |
| void | generateParameters_ (const Param ¶m, const Map< String, Option > &options, std::vector< Param > ¶meters) |
| void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. | |
Protected Attributes | |
| Map< String, Option > | cv_options_ |
| PeakSpectrumCompareFunctor * | pscf_ |
Detailed Description
Implementation of a cross valdidation training for the PILIS model.
This class serves as an implementation of a cross validation training for the PILIS model. It includes a range of parameters which can be set to perform a GridSearch additionally.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| nfold | int | 10 | Number of partitions to use for cross validation | |
| optimization_method | string | tophit_against_all_others | tophit_against_all_others, only_top_hit, top_n_ions, top_n_ions_by | Scoring method used for optimization |
| compare_function | string | SpectrumAlignmentScore | SpectrumAlignmentScore, ZhangSimilarityScore | Spectra scoring function to use |
| num_top_peaks | int | 2 | Number of highest abundant peaks to consider with top_n_ion and top_n_ions_by optimization_methods | |
| min_intensity | float | 0.3 | Min relative intensity of highest abundant peaks to consider in top_n_ions_by | |
| fragment_mass_tolerance | float | 0.5 | Fragment mass tolerance, mainly used in compare function. | |
| normalize_to_TIC | string | true | true, false | Whether the spectra should be normalized to TIC before training, to max of one otherwise. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
Default constructor.
| PILISCrossValidation | ( | const PILISCrossValidation & | rhs | ) |
copy constructor
| virtual ~PILISCrossValidation | ( | ) | [virtual] |
desctructor
Member Function Documentation
| void apply | ( | Param & | PILIS_param, | |
| const PILISModel & | base_model, | |||
| const std::vector< Peptide > & | peptides | |||
| ) |
performs a cross validation and write optimized param into PILIS_param
| void generateParameters_ | ( | const Param & | param, | |
| const Map< String, Option > & | options, | |||
| std::vector< Param > & | parameters | |||
| ) | [protected] |
| PILISCrossValidation& operator= | ( | const PILISCrossValidation & | rhs | ) |
assignment operator
| void partition_ | ( | std::vector< std::vector< Peptide > > & | parts, | |
| const std::vector< Peptide > & | source | |||
| ) | [protected] |
| DoubleReal scoreHits | ( | const std::vector< std::vector< std::vector< RichPeakSpectrum > > > & | sim_spectra, | |
| const std::vector< std::vector< RichPeakSpectrum > > & | exp_spectra | |||
| ) |
compares experimental and simulated spectra and returns a score
| DoubleReal scoreSpectra_ | ( | const RichPeakSpectrum & | spec1, | |
| const RichPeakSpectrum & | spec2 | |||
| ) | [protected] |
sets a option to be used for the cross validation
sets the options which should be used for the cross validation
| void updateMembers_ | ( | ) | [protected, virtual] |
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
Map<String, Option> cv_options_ [protected] |
PeakSpectrumCompareFunctor* pscf_ [protected] |
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |