OpenMS  3.0.0
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 
63  IsobaricNormalizer& operator=(const IsobaricNormalizer& rhs);
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 
101  void collectRatios_(const ConsensusFeature& cf,
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 
OpenMS::IsobaricNormalizer::peptide_intensities_
std::vector< std::vector< Peak2D::IntensityType > > peptide_intensities_
Collection containing the collected peptide intensities for the individual channels.
Definition: IsobaricNormalizer.h:121
Types.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsobaricNormalizer::quant_meth_
const IsobaricQuantitationMethod * quant_meth_
The selected quantitation method that will be used for the normalization.
Definition: IsobaricNormalizer.h:74
OpenMS::IsobaricNormalizer::map_to_vec_index_
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
OpenMS::IsobaricNormalizer
Performs median normalization on the extracted ratios of isobaric labeling experiment.
Definition: IsobaricNormalizer.h:53
OpenMS::IsobaricNormalizer::ref_map_id_
Size ref_map_id_
The index of the reference channel in the peptide ratio/intensity vectors.
Definition: IsobaricNormalizer.h:115
ConsensusFeature.h
IsobaricQuantifierStatistics.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Peak2D.h
OpenMS::IsobaricNormalizer::reference_channel_name_
String reference_channel_name_
The name of the reference channel as given in the IsobaricChannelInformation.
Definition: IsobaricNormalizer.h:77
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
float
OpenMS::IsobaricNormalizer::peptide_ratios_
std::vector< std::vector< Peak2D::IntensityType > > peptide_ratios_
Collection containing the collected peptide ratios for the individual channels.
Definition: IsobaricNormalizer.h:118
String.h
OpenSwath::normalize
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.