This class actually implements the E-value based scoring of PILIS. More...
#include <OpenMS/ANALYSIS/ID/PILISScoring.h>
Public Member Functions | |
PILISScoring & | operator= (const PILISScoring &source) |
constructors and destructors | |
PILISScoring () | |
default constructor More... | |
PILISScoring (const PILISScoring &source) | |
copy constructor More... | |
virtual | ~PILISScoring () |
destructor More... | |
Accessors | |
void | getScores (std::vector< PeptideIdentification > &ids) |
performs an ProteinIdentification run on a PeakMap More... | |
void | getScore (PeptideIdentification &id) |
performs an ProteinIdentification run on a PeakSpectrum More... | |
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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 Member Functions | |
void | getFitParameter_ (double &slope, double &intercept, const std::vector< double > &scores, double threshold) |
void | getSurvivalFunction_ (Map< UInt, double > &points, std::vector< DPosition< 2 > > &survival_function) |
void | getScore_ (PeptideIdentification &id, double global_slope, double global_intercept) |
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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 | |
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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... | |
This class actually implements the E-value based scoring of PILIS.
The method which is used to generate the E-values are adapted from
David Fenyo and Ronald C. Beavis Anal. Chem. 2003, 75, 768-774 A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes.
The bases for the calculation are the similarity scores of the simulated and experimental spectra. The scores are transformed into a discrete score distribution and from this distribution E-values are calculated for the peptide hits.
If more than one spectrum is given two E-values can be calculated, one which gives the significance of the peptide hit considering only one spectrum, and the other also considering also all other hits of all other spectra. The second type of scoring is somewhat more accurate.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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use_local_scoring | int | 1 | If set to 1, a E-Value of an identification run of one spectrum is used additionally | |
survival_function_bin_size | int | 20 | Bin size of the survival function | |
global_linear_fitting_threshold | float | 0.1 | Fitting threshold of the survival function of the global E-Value calculation | |
local_linear_fitting_threshold | float | 0.5 | Fitting threshold of the survival function of the local E-Value calculation | |
score_default_value | float | 100000000000 | If no score can be assigned use this one |
PILISScoring | ( | ) |
default constructor
PILISScoring | ( | const PILISScoring & | source | ) |
copy constructor
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virtual |
destructor
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protected |
void getScore | ( | PeptideIdentification & | id | ) |
performs an ProteinIdentification run on a PeakSpectrum
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protected |
void getScores | ( | std::vector< PeptideIdentification > & | ids | ) |
performs an ProteinIdentification run on a PeakMap
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protected |
PILISScoring& operator= | ( | const PILISScoring & | source | ) |
OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:39 using doxygen 1.8.9.1 |