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IsobaricIsotopeCorrector.h
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31 // $Maintainer: Stephan Aiche $
32 // $Authors: Stephan Aiche, Chris Bielow $
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34 
35 #ifndef OPENMS_ANALYSIS_QUANTITATION_ISOBARICISOTOPECORRECTOR_H
36 #define OPENMS_ANALYSIS_QUANTITATION_ISOBARICISOTOPECORRECTOR_H
37 
39 
42 
43 namespace OpenMS
44 {
48  class OPENMS_DLLAPI IsobaricIsotopeCorrector
49  {
50 public:
56  IsobaricIsotopeCorrector(const IsobaricQuantitationMethod* const quant_method);
57 
60 
63 
64  virtual ~IsobaricIsotopeCorrector();
65 
75  IsobaricQuantifierStatistics correctIsotopicImpurities(const ConsensusMap& consensus_map_in, ConsensusMap& consensus_map_out);
76 
77 private:
80 
83  gsl_matrix* gsl_m_;
84  gsl_permutation* gsl_p_;
85  gsl_vector* gsl_b_;
86  gsl_vector* gsl_x_;
87 
90 
92  void freeGSLMemory_();
94 
101  bool isIdentityMatrix_(const Matrix<double>& channel_frequency) const;
102 
108  bool isInvertible_() const;
109 
113  void fillInputVector_(gsl_vector* gsl_b, Matrix<double>& m_b, const ConsensusFeature& cf, const ConsensusMap& cm) const;
114 
118  void solveGSL_(const gsl_matrix* gsl_m, const gsl_permutation* gsl_p, const gsl_vector* gsl_b, gsl_vector* gsl_x) const;
119 
123  void solveNNLS_(const Matrix<double>& correction_matrix, const Matrix<double>& m_b, Matrix<double>& m_x) const;
124 
128  void computeStats_(const Matrix<double>& m_x, gsl_vector* gsl_x, const ConsensusFeature::IntensityType cf_intensity, IsobaricQuantifierStatistics& stats);
129 
133  ConsensusFeature::IntensityType updateOutpuMap_(const ConsensusMap& consensus_map_in, ConsensusMap& consensus_map_out, ConsensusMap::size_type current_cf, const Matrix<double>& m_x) const;
134  };
135 } // namespace
136 
137 #endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICISOTOPECORRECTOR_H
Real IntensityType
Intensity type.
Definition: Peak2D.h:63
gsl_permutation * gsl_p_
Definition: IsobaricIsotopeCorrector.h:84
A container for consensus elements.
Definition: ConsensusMap.h:60
gsl_vector * gsl_b_
Definition: IsobaricIsotopeCorrector.h:85
gsl_matrix * gsl_m_
GSL objects used for the isotope correction.
Definition: IsobaricIsotopeCorrector.h:83
Performs isotope impurity correction on the intensities extracted from an isobaric labeling experimen...
Definition: IsobaricIsotopeCorrector.h:48
bool gsl_allocated_
Indicates wether memory was allocated for the gsl vector/matrix pointers.
Definition: IsobaricIsotopeCorrector.h:89
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...
Definition: IsobaricQuantifierStatistics.h:47
const IsobaricQuantitationMethod * quant_method_
The quantification method used for the dataset to be analyzed.
Definition: IsobaricIsotopeCorrector.h:79
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:51
gsl_vector * gsl_x_
Definition: IsobaricIsotopeCorrector.h:86
A 2-dimensional consensus feature.
Definition: ConsensusFeature.h:59

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5