OpenMS
IsobaricNormalizer.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche, Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/KERNEL/Peak2D.h>
42 
43 #include <map>
44 
45 namespace OpenMS
46 {
47  class IsobaricQuantitationMethod;
48  class ConsensusMap;
49 
53  class OPENMS_DLLAPI IsobaricNormalizer
54  {
55 public:
57  explicit IsobaricNormalizer(const IsobaricQuantitationMethod* const quant_method);
58 
61 
64 
70  void normalize(ConsensusMap& consensus_map);
71 
72 private:
75 
78 
86  ConsensusFeature::HandleSetType::iterator findReferenceChannel_(ConsensusFeature& cf, const ConsensusMap& consensus_map) const;
87 
93  void buildVectorIndex_(const ConsensusMap& consensus_map);
94 
102  const Peak2D::IntensityType& ref_intensity);
103 
109  void computeNormalizationFactors_(std::vector<Peak2D::IntensityType>& normalization_factors);
110 
112  std::map<Size, Size> map_to_vec_index_;
113 
116 
118  std::vector<std::vector<Peak2D::IntensityType> > peptide_ratios_;
119 
121  std::vector<std::vector<Peak2D::IntensityType> > peptide_intensities_;
122 
123  };
124 } // namespace
125 
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:71
A container for consensus elements.
Definition: ConsensusMap.h:92
Performs median normalization on the extracted ratios of isobaric labeling experiment.
Definition: IsobaricNormalizer.h:54
void buildVectorIndex_(const ConsensusMap &consensus_map)
Constructs a mapping from file description to the index in the corresponding ratio/intensity vectors.
void collectRatios_(const ConsensusFeature &cf, const Peak2D::IntensityType &ref_intensity)
Collects ratios and intensities for a given ConsensusFeature.
String reference_channel_name_
The name of the reference channel as given in the IsobaricChannelInformation.
Definition: IsobaricNormalizer.h:77
void computeNormalizationFactors_(std::vector< Peak2D::IntensityType > &normalization_factors)
Computes the normalization factors from the given peptide ratios.
ConsensusFeature::HandleSetType::iterator findReferenceChannel_(ConsensusFeature &cf, const ConsensusMap &consensus_map) const
Given a ConsensusFeature the method will return an iterator pointing to the consensus element represe...
void normalize(ConsensusMap &consensus_map)
Normalizes the intensity ratios in the given input map (using median).
IsobaricNormalizer & operator=(const IsobaricNormalizer &rhs)
Assignment operator.
Size ref_map_id_
The index of the reference channel in the peptide ratio/intensity vectors.
Definition: IsobaricNormalizer.h:115
std::vector< std::vector< Peak2D::IntensityType > > peptide_ratios_
Collection containing the collected peptide ratios for the individual channels.
Definition: IsobaricNormalizer.h:118
IsobaricNormalizer(const IsobaricNormalizer &other)
Copy c'tor.
IsobaricNormalizer(const IsobaricQuantitationMethod *const quant_method)
Default c'tor.
std::vector< std::vector< Peak2D::IntensityType > > peptide_intensities_
Collection containing the collected peptide intensities for the individual channels.
Definition: IsobaricNormalizer.h:121
std::map< Size, Size > map_to_vec_index_
The mapping between map indices and the corresponding indices in the peptide ratio/intensity vectors.
Definition: IsobaricNormalizer.h:112
const IsobaricQuantitationMethod * quant_meth_
The selected quantitation method that will be used for the normalization.
Definition: IsobaricNormalizer.h:74
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:58
float IntensityType
Intensity type.
Definition: Peak2D.h:62
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48