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 | |
| PILISScoring (const PILISScoring &source) | |
| copy constructor | |
| virtual | ~PILISScoring () |
| destructor | |
Accessors | |
| void | getScores (std::vector< PeptideIdentification > &ids) |
| performs an ProteinIdentification run on a PeakMap | |
| void | getScore (PeptideIdentification &id) |
| performs an ProteinIdentification run on a PeakSpectrum | |
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) |
Detailed Description
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 tranformed 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 |
|---|---|---|---|---|
| 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 |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
| PILISScoring | ( | ) |
default constructor
| PILISScoring | ( | const PILISScoring & | source | ) |
copy constructor
| virtual ~PILISScoring | ( | ) | [virtual] |
destructor
Member Function Documentation
| void getFitParameter_ | ( | double & | slope, | |
| double & | intercept, | |||
| const std::vector< double > & | scores, | |||
| double | threshold | |||
| ) | [protected] |
| void getScore | ( | PeptideIdentification & | id | ) |
performs an ProteinIdentification run on a PeakSpectrum
| void getScore_ | ( | PeptideIdentification & | id, | |
| double | global_slope, | |||
| double | global_intercept | |||
| ) | [protected] |
| void getScores | ( | std::vector< PeptideIdentification > & | ids | ) |
performs an ProteinIdentification run on a PeakMap
| void getSurvivalFunction_ | ( | Map< UInt, double > & | points, | |
| std::vector< DPosition< 2 > > & | survival_function | |||
| ) | [protected] |
| PILISScoring& operator= | ( | const PILISScoring & | source | ) |
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |