libpappsomspp
Library for mass spectrometry
pappso::IonIsotopeRatioScore Class Reference

#include <ionisotoperatioscore.h>

Public Member Functions

 IonIsotopeRatioScore (const MassSpectrum &spectrum, const PeptideSp &peptide_sp, unsigned int parent_charge, PrecisionPtr precision, std::vector< PeptideIon > ion_list)
 
virtual ~IonIsotopeRatioScore ()
 
pappso::pappso_double getIonIsotopeRatioScore () const
 

Private Attributes

pappso::pappso_double m_ionIsotopeRatioScore
 

Detailed Description

Definition at line 36 of file ionisotoperatioscore.h.

Constructor & Destructor Documentation

◆ IonIsotopeRatioScore()

IonIsotopeRatioScore::IonIsotopeRatioScore ( const MassSpectrum spectrum,
const PeptideSp peptide_sp,
unsigned int  parent_charge,
PrecisionPtr  precision,
std::vector< PeptideIon ion_list 
)

Definition at line 34 of file ionisotoperatioscore.cpp.

39 {
40  std::list<PeptideIon> ion_list(ion_vector.begin(), ion_vector.end());
42  spectrum, peptide_sp, parent_charge, precision, ion_list, 1, 1);
43 
44  Trace scaterplot;
45 
46  for(PeptideIon ion_type : ion_vector)
47  {
48  std::vector<double> mono_th_intensities(peptide_sp.get()->size(), 0);
49  std::vector<double> isotope_th_intensities(peptide_sp.get()->size(), 0);
50 
51  std::vector<double> mono_exp_intensities(peptide_sp.get()->size(), 0);
52  std::vector<double> isotope_exp_intensities(peptide_sp.get()->size(), 0);
53  for(const PeakIonIsotopeMatch &peak_ion_match :
54  psm_match.getPeakIonIsotopeMatchList())
55  {
56  if(peak_ion_match.getPeptideIonType() == ion_type)
57  {
58  std::size_t vector_position =
59  peak_ion_match.getPeptideFragmentIonSp().get()->size() - 1;
60  PeptideNaturalIsotopeAverageSp iso_average_sp =
61  peak_ion_match.getPeptideNaturalIsotopeAverageSp();
62  if(iso_average_sp.get()->getIsotopeNumber() == 0)
63  {
64  mono_th_intensities[vector_position] =
65  iso_average_sp.get()->getIntensityRatio();
66  mono_exp_intensities[vector_position] =
67  peak_ion_match.getPeak().y;
68  }
69  else if(iso_average_sp.get()->getIsotopeNumber() == 1)
70  {
71  isotope_th_intensities[vector_position] =
72  iso_average_sp.get()->getIntensityRatio();
73  isotope_exp_intensities[vector_position] =
74  peak_ion_match.getPeak().y;
75  }
76  }
77  }
78 
79  for(std::size_t i = 0; i < mono_th_intensities.size(); i++)
80  {
81  if((mono_th_intensities[i] != 0) && (isotope_th_intensities[i] != 0))
82  {
83  DataPoint xy(mono_th_intensities[i] / isotope_th_intensities[i],
84  mono_exp_intensities[i] /
85  isotope_exp_intensities[i]);
86  scaterplot.push_back(xy);
87  }
88  }
89  }
90 
91  scaterplot.sortX();
92 
93  LinearRegression linear_regression(scaterplot);
94 
96  linear_regression.getCoefficientOfDetermination(scaterplot);
97 }
pappso::pappso_double m_ionIsotopeRatioScore
A simple container of DataPoint instances.
Definition: trace.h:148
void sortX()
Definition: trace.cpp:956
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:386
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp

References pappso::LinearRegression::getCoefficientOfDetermination(), pappso::PeptideIsotopeSpectrumMatch::getPeakIonIsotopeMatchList(), m_ionIsotopeRatioScore, pappso::Trace::sortX(), and pappso::xy.

◆ ~IonIsotopeRatioScore()

IonIsotopeRatioScore::~IonIsotopeRatioScore ( )
virtual

Definition at line 100 of file ionisotoperatioscore.cpp.

101 {
102 }

Member Function Documentation

◆ getIonIsotopeRatioScore()

pappso::pappso_double IonIsotopeRatioScore::getIonIsotopeRatioScore ( ) const

Definition at line 105 of file ionisotoperatioscore.cpp.

106 {
107  return m_ionIsotopeRatioScore;
108 }

References m_ionIsotopeRatioScore.

Member Data Documentation

◆ m_ionIsotopeRatioScore

pappso::pappso_double pappso::IonIsotopeRatioScore::m_ionIsotopeRatioScore
private

Definition at line 49 of file ionisotoperatioscore.h.

Referenced by IonIsotopeRatioScore(), and getIonIsotopeRatioScore().


The documentation for this class was generated from the following files: