OpenMS  3.0.0
IsobaricIsotopeCorrector.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche, Chris Bielow $
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34 
35 #pragma once
36 
38 
39 // forward decl
40 namespace Eigen
41 {
42  template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
43  class Matrix;
44  using MatrixXd = Matrix<double, -1, -1, 0, -1, -1>;
45  using VectorXd = Matrix<double, -1, 1, 0, -1, 1>;
46 }
47 
48 namespace OpenMS
49 {
50  class IsobaricQuantitationMethod;
51  class IsobaricQuantifierStatistics;
52  class ConsensusMap;
53  class ConsensusFeature;
54 
58  class OPENMS_DLLAPI IsobaricIsotopeCorrector
59  {
60 public:
71  static IsobaricQuantifierStatistics correctIsotopicImpurities(const ConsensusMap& consensus_map_in,
72  ConsensusMap& consensus_map_out,
73  const IsobaricQuantitationMethod* quant_method);
74 
75 private:
79  static void fillInputVector_(Eigen::VectorXd& b,
80  Matrix<double>& m_b,
81  const ConsensusFeature& cf,
82  const ConsensusMap& cm);
83 
87  static void solveNNLS_(const Matrix<double>& correction_matrix,
88  const Matrix<double>& m_b, Matrix<double>& m_x);
89 
93  static void computeStats_(const Matrix<double>& m_x,
94  const Eigen::MatrixXd& x,
95  const float cf_intensity,
96  const IsobaricQuantitationMethod* quant_method,
98 
102  static float updateOutpuMap_(const ConsensusMap& consensus_map_in,
103  ConsensusMap& consensus_map_out,
104  Size current_cf,
105  const Matrix<double>& m_x);
106  };
107 } // namespace
108 
Eigen
Definition: IsobaricIsotopeCorrector.h:40
double
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Matrix.h
OpenMS::IsobaricQuantifierStatistics
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...
Definition: IsobaricQuantifierStatistics.h:48
Eigen::Matrix
Definition: IsobaricIsotopeCorrector.h:43
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Matrix< double >
OpenMS::IsobaricQuantitationMethod
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:55
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::IsobaricIsotopeCorrector
Performs isotope impurity correction on the intensities extracted from an isobaric labeling experimen...
Definition: IsobaricIsotopeCorrector.h:58