OpenMS
IsobaricIsotopeCorrector.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Stephan Aiche, Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 
13 // forward decl
14 namespace Eigen
15 {
16  template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
17  class Matrix;
18  using MatrixXd = Matrix<double, -1, -1, 0, -1, -1>;
19  using VectorXd = Matrix<double, -1, 1, 0, -1, 1>;
20 }
21 
22 namespace OpenMS
23 {
24  class IsobaricQuantitationMethod;
25  class IsobaricQuantifierStatistics;
26  class ConsensusMap;
27  class ConsensusFeature;
28 
32  class OPENMS_DLLAPI IsobaricIsotopeCorrector
33  {
34 public:
46  ConsensusMap& consensus_map_out,
47  const IsobaricQuantitationMethod* quant_method);
48 
49 private:
54  Matrix<double>& m_b,
55  const ConsensusFeature& cf,
56  const ConsensusMap& cm);
57 
61  static void solveNNLS_(const Matrix<double>& correction_matrix,
62  const Matrix<double>& m_b, Matrix<double>& m_x);
63 
67  static void computeStats_(const Matrix<double>& m_x,
68  const Eigen::MatrixXd& x,
69  const float cf_intensity,
70  const IsobaricQuantitationMethod* quant_method,
72 
76  static float updateOutpuMap_(const ConsensusMap& consensus_map_in,
77  ConsensusMap& consensus_map_out,
78  Size current_cf,
79  const Matrix<double>& m_x);
80  };
81 } // namespace
82 
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:45
A container for consensus elements.
Definition: ConsensusMap.h:66
Performs isotope impurity correction on the intensities extracted from an isobaric labeling experimen...
Definition: IsobaricIsotopeCorrector.h:33
static void fillInputVector_(Eigen::VectorXd &b, Matrix< double > &m_b, const ConsensusFeature &cf, const ConsensusMap &cm)
Fills the input vector for the Eigen/NNLS step given the ConsensusFeature.
static void computeStats_(const Matrix< double > &m_x, const Eigen::MatrixXd &x, const float cf_intensity, const IsobaricQuantitationMethod *quant_method, IsobaricQuantifierStatistics &stats)
static IsobaricQuantifierStatistics correctIsotopicImpurities(const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, const IsobaricQuantitationMethod *quant_method)
Apply isotope correction to the given input map and store the corrected values in the output map.
static float updateOutpuMap_(const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, Size current_cf, const Matrix< double > &m_x)
static void solveNNLS_(const Matrix< double > &correction_matrix, const Matrix< double > &m_b, Matrix< double > &m_x)
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...
Definition: IsobaricQuantifierStatistics.h:23
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:32
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:101
Definition: IsobaricIsotopeCorrector.h:15
Definition: IsobaricIsotopeCorrector.h:17
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22