libpappsomspp
Library for mass spectrometry
ionisotoperatioscore.cpp
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1 /**
2  * \file pappsomspp/psm/experimental/ionisotoperatioscore.cpp
3  * \date 18/05/2019
4  * \author Olivier Langella
5  * \brief psm score computed using ion isotopes
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  ******************************************************************************/
27 
28 #include "ionisotoperatioscore.h"
29 #include "../peptideisotopespectrummatch.h"
30 #include "../../trace/linearregression.h"
31 
32 using namespace pappso;
33 
35  const PeptideSp &peptide_sp,
36  unsigned int parent_charge,
37  PrecisionPtr precision,
38  std::vector<PeptideIon> ion_vector)
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 }
98 
99 
101 {
102 }
103 
106 {
107  return m_ionIsotopeRatioScore;
108 }
pappso::pappso_double getIonIsotopeRatioScore() const
IonIsotopeRatioScore(const MassSpectrum &spectrum, const PeptideSp &peptide_sp, unsigned int parent_charge, PrecisionPtr precision, std::vector< PeptideIon > ion_list)
pappso::pappso_double m_ionIsotopeRatioScore
double getCoefficientOfDetermination(const Trace &data) const
get Coefficient of determination (R2)
Class to represent a mass spectrum.
Definition: massspectrum.h:71
const std::list< PeakIonIsotopeMatch > & getPeakIonIsotopeMatchList() const
A simple container of DataPoint instances.
Definition: trace.h:148
void sortX()
Definition: trace.cpp:956
psm score computed using ion isotopes
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:386
std::shared_ptr< const Peptide > PeptideSp
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp