HyperScore Struct Reference

An implementation of the X!Tandem HyperScore PSM scoring function. More...

#include <OpenMS/ANALYSIS/ID/HyperScore.h>

Classes
struct	PSMDetail
	compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match More...

Public Types
typedef std::pair< Size, double >	IndexScorePair

Static Public Member Functions
static double	compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum)
	compute the (ln transformed) X!Tandem HyperScore More...
static double	computeWithDetail (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum, PSMDetail &d)
static double	compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges, const PeakSpectrum &theo_spectrum, const DataArrays::IntegerDataArray &theo_charges)
static double	compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges, const PeakSpectrum &theo_spectrum, const DataArrays::IntegerDataArray &theo_charges, std::vector< double > &intensity_sum)

Static Private Member Functions
static double	logfactorial_ (const int x, int base=2)
	helper to compute the log factorial More...

Detailed Description

An implementation of the X!Tandem HyperScore PSM scoring function.

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Class Documentation

OpenMS::HyperScore::PSMDetail

struct OpenMS::HyperScore::PSMDetail

compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match

Collaboration diagram for HyperScore::PSMDetail:

Class Members
size_t	matched_b_ions
size_t	matched_y_ions
double	mean_error

Member Typedef Documentation

IndexScorePair

typedef std::pair<Size, double> IndexScorePair

Member Function Documentation

compute() [1/3]

static double compute ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const DataArrays::IntegerDataArray &  exp_charges, const PeakSpectrum &  theo_spectrum, const DataArrays::IntegerDataArray &  theo_charges  )

static

compute() [2/3]

static double compute ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const DataArrays::IntegerDataArray &  exp_charges, const PeakSpectrum &  theo_spectrum, const DataArrays::IntegerDataArray &  theo_charges, std::vector< double > &  intensity_sum  )

static

compute() [3/3]

static double compute ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const PeakSpectrum &  theo_spectrum  )

static

compute the (ln transformed) X!Tandem HyperScore

1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated
2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions

   Note

   Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities

   Parameters

   fragment_mass_tolerance	mass tolerance applied left and right of the theoretical spectrum peak position
   fragment_mass_tolerance_unit_ppm	Unit of the mass tolerance is: Thomson if false, ppm if true
   exp_spectrum	measured spectrum
   theo_spectrum	theoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator.

computeWithDetail()

static double computeWithDetail ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const PeakSpectrum &  theo_spectrum, PSMDetail &  d  )

static

logfactorial_()

static double logfactorial_ ( const int  x, int  base = 2  )

staticprivate

helper to compute the log factorial