#include <OpenMS/ANALYSIS/ID/PILISScoring.h>
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.
PILISScoring Parameters are explained on a separate page.
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_ (HashMap< UInt, double > &points, std::vector< DPosition< 2 > > &survival_function) |
void | getScore_ (PeptideIdentification &id, double global_slope, double global_intercept) |
PILISScoring | ( | ) |
default constructor
PILISScoring | ( | const PILISScoring & | source | ) |
copy constructor
virtual ~PILISScoring | ( | ) | [virtual] |
destructor
PILISScoring& operator= | ( | const PILISScoring & | source | ) |
void getScores | ( | std::vector< PeptideIdentification > & | ids | ) |
performs an ProteinIdentification run on a PeakMap
void getScore | ( | PeptideIdentification & | id | ) |
performs an ProteinIdentification run on a PeakSpectrum
void getFitParameter_ | ( | double & | slope, | |
double & | intercept, | |||
const std::vector< double > & | scores, | |||
double | threshold | |||
) | [protected] |
void getSurvivalFunction_ | ( | HashMap< UInt, double > & | points, | |
std::vector< DPosition< 2 > > & | survival_function | |||
) | [protected] |
void getScore_ | ( | PeptideIdentification & | id, | |
double | global_slope, | |||
double | global_intercept | |||
) | [protected] |
Generated Tue Apr 1 15:36:41 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |