OpenMS
IsobaricNormalizer.h
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1 // Copyright (c) 2002-present, 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 
11 #include <OpenMS/CONCEPT/Types.h>
13 #include <OpenMS/KERNEL/Peak2D.h>
16 
17 #include <map>
18 
19 namespace OpenMS
20 {
21  class IsobaricQuantitationMethod;
22  class ConsensusMap;
23 
27  class OPENMS_DLLAPI IsobaricNormalizer
28  {
29 public:
31  explicit IsobaricNormalizer(const IsobaricQuantitationMethod* const quant_method);
32 
35 
38 
44  void normalize(ConsensusMap& consensus_map);
45 
46 private:
49 
52 
60  ConsensusFeature::HandleSetType::iterator findReferenceChannel_(ConsensusFeature& cf, const ConsensusMap& consensus_map) const;
61 
67  void buildVectorIndex_(const ConsensusMap& consensus_map);
68 
76  const Peak2D::IntensityType& ref_intensity);
77 
83  void computeNormalizationFactors_(std::vector<Peak2D::IntensityType>& normalization_factors);
84 
86  std::map<Size, Size> map_to_vec_index_;
87 
90 
92  std::vector<std::vector<Peak2D::IntensityType> > peptide_ratios_;
93 
95  std::vector<std::vector<Peak2D::IntensityType> > peptide_intensities_;
96 
97  };
98 } // namespace
99 
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:45
A container for consensus elements.
Definition: ConsensusMap.h:66
Performs median normalization on the extracted ratios of isobaric labeling experiment.
Definition: IsobaricNormalizer.h:28
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:51
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:89
std::vector< std::vector< Peak2D::IntensityType > > peptide_ratios_
Collection containing the collected peptide ratios for the individual channels.
Definition: IsobaricNormalizer.h:92
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:95
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:86
const IsobaricQuantitationMethod * quant_meth_
The selected quantitation method that will be used for the normalization.
Definition: IsobaricNormalizer.h:48
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:32
float IntensityType
Intensity type.
Definition: Peak2D.h:36
A more convenient string class.
Definition: String.h:34
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19