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IsobaricNormalizer.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
39 #include <OpenMS/DATASTRUCTURES/Map.h>
40 #include <OpenMS/KERNEL/Peak2D.h>
41 #include <OpenMS/KERNEL/ConsensusFeature.h>
42 #include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifierStatistics.h>
43
44 namespace OpenMS
45 {
46 class IsobaricQuantitationMethod;
47 class ConsensusMap;
48
52 class OPENMS_DLLAPI IsobaricNormalizer
53 {
54 public:
56 explicit IsobaricNormalizer(const IsobaricQuantitationMethod* const quant_method);
57
59 IsobaricNormalizer(const IsobaricNormalizer& other);
60
62 IsobaricNormalizer& operator=(const IsobaricNormalizer& rhs);
63
69 void normalize(ConsensusMap& consensus_map);
70
71 private:
73 const IsobaricQuantitationMethod* quant_meth_;
74
76 String reference_channel_name_;
77
85 ConsensusFeature::HandleSetType::iterator findReferenceChannel_(ConsensusFeature& cf, const ConsensusMap& consensus_map) const;
86
92 void buildVectorIndex_(const ConsensusMap& consensus_map);
93
100 void collectRatios_(const ConsensusFeature& cf,
101 const Peak2D::IntensityType& ref_intensity);
102
108 void computeNormalizationFactors_(std::vector<Peak2D::IntensityType>& normalization_factors);
109
111 Map<Size, Size> map_to_vec_index_;
112
114 Size ref_map_id_;
115
117 std::vector<std::vector<Peak2D::IntensityType> > peptide_ratios_;
118
120 std::vector<std::vector<Peak2D::IntensityType> > peptide_intensities_;
121
122 };
123 } // namespace
124
OpenMS::IsobaricNormalizer::map_to_vec_index_
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:111
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IsobaricQuantitationMethod
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:54
Types.h
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
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:120
String.h
OpenMS::Map< Size, Size >
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Peak2D.h
OpenMS::IsobaricNormalizer
Performs median normalization on the extracted ratios of isobaric labeling experiment.
Definition: IsobaricNormalizer.h:52
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.
Map.h
ConsensusFeature.h
float
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::IsobaricNormalizer::reference_channel_name_
String reference_channel_name_
The name of the reference channel as given in the IsobaricChannelInformation.
Definition: IsobaricNormalizer.h:76
IsobaricQuantifierStatistics.h
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:117
OpenMS::IsobaricNormalizer::quant_meth_
const IsobaricQuantitationMethod * quant_meth_
The selected quantitation method that will be used for the normalization.
Definition: IsobaricNormalizer.h:73
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsobaricNormalizer::ref_map_id_
Size ref_map_id_
The index of the reference channel in the peptide ratio/intensity vectors.
Definition: IsobaricNormalizer.h:114