PScore Struct Reference

Implementation of the PScore PSM scoring algorithm. More...

#include <OpenMS/ANALYSIS/RNPXL/PScore.h>

Static Public Member Functions
static std::vector< Size >	calculateIntensityRankInMZWindow (const std::vector< double > &mz, const std::vector< double > &intensities, double mz_window)
static std::vector< std::vector< Size > >	calculateRankMap (const PeakMap &peak_map, double mz_window=100)
static std::map< Size, PeakSpectrum >	calculatePeakLevelSpectra (const PeakSpectrum &spec, const std::vector< Size > &ranks, Size min_level=1, Size max_level=9)
static double	computePScore (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &peak_level_spectra, const std::vector< PeakSpectrum > &theo_spectra, double mz_window=100.0)
static double	computePScore (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &peak_level_spectra, const PeakSpectrum &theo_spectrum, double mz_window=100.0)
static double	massCorrectionTerm (double mass)
static double	cleavageCorrectionTerm (Size cleavages, bool consecutive_cleavage)
static double	modificationCorrectionTerm (Size modifications)

Detailed Description

Implementation of the PScore PSM scoring algorithm.

Member Function Documentation

calculateIntensityRankInMZWindow()

static std::vector<Size> calculateIntensityRankInMZWindow ( const std::vector< double > &  mz, const std::vector< double > &  intensities, double  mz_window  )

static

calculatePeakLevelSpectra()

static std::map<Size, PeakSpectrum > calculatePeakLevelSpectra ( const PeakSpectrum &  spec, const std::vector< Size > &  ranks, Size  min_level = 1, Size  max_level = 9  )

static

calculateRankMap()

static std::vector<std::vector<Size> > calculateRankMap ( const PeakMap &  peak_map, double  mz_window = 100  )

static

cleavageCorrectionTerm()

static double cleavageCorrectionTerm ( Size  cleavages, bool  consecutive_cleavage  )

static

correction term for type of cleavage. For reference see the Andromeda source code.

Note

: constants used in the correction term might be instrument dependent

computePScore() [1/2]

static double computePScore ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &  peak_level_spectra, const std::vector< PeakSpectrum > &  theo_spectra, double  mz_window = 100.0  )

static

computePScore() [2/2]

static double computePScore ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const std::map< Size, PeakSpectrum > &  peak_level_spectra, const PeakSpectrum &  theo_spectrum, double  mz_window = 100.0  )

static

massCorrectionTerm()

static double massCorrectionTerm ( double  mass )

static

additive correction terms used by Andromeda (pscore + massC + cleaveC + modC - 100). For reference see the Andromeda source code.

Note

: constants used in the correction term might be instrument dependent

modificationCorrectionTerm()

static double modificationCorrectionTerm ( Size  modifications )

static

correction term for modification. For reference see the Andromeda source code.

Note

: constants used in the correction term might be instrument dependent