OpenMS
IsobaricQuantifier.h
Go to the documentation of this file.
1 // Copyright (c) 2002-2023, 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 
13 
14 namespace OpenMS
15 {
16  class IsobaricQuantitationMethod;
17  class ConsensusMap;
18 
25  class OPENMS_DLLAPI IsobaricQuantifier :
26  public DefaultParamHandler
27  {
28 public:
34  explicit IsobaricQuantifier(const IsobaricQuantitationMethod* const quant_method);
35 
38 
41 
51  void quantify(const ConsensusMap& consensus_map_in, ConsensusMap& consensus_map_out);
52 
53 protected:
56 
58  void updateMembers_() override;
59 
60 private:
63 
66 
69 
72 
74  void computeLabelingStatistics_(ConsensusMap& consensus_map_out);
75  };
76 } // namespace
77 
A container for consensus elements.
Definition: ConsensusMap.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...
Definition: IsobaricQuantifierStatistics.h:23
Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensitie...
Definition: IsobaricQuantifier.h:27
bool isotope_correction_enabled_
Is true if isotope correction is enabled, false otherwise.
Definition: IsobaricQuantifier.h:68
const IsobaricQuantitationMethod * quant_method_
The quantification method used for the dataset to be analyzed.
Definition: IsobaricQuantifier.h:65
void setDefaultParams_()
implemented for DefaultParamHandler
IsobaricQuantifier(const IsobaricQuantitationMethod *const quant_method)
Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex).
IsobaricQuantifier(const IsobaricQuantifier &other)
Copy c'tor.
IsobaricQuantifierStatistics stats_
Stats of current quantitation run.
Definition: IsobaricQuantifier.h:62
IsobaricQuantifier & operator=(const IsobaricQuantifier &rhs)
Assignment operator.
void quantify(const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out)
Using the raw isobaric intensities we apply isotope correction, normalization (using median).
void updateMembers_() override
implemented for DefaultParamHandler
void computeLabelingStatistics_(ConsensusMap &consensus_map_out)
Computes labeling statistics (efficiency, number of empty scans,...)
bool normalization_enabled_
Is true if normalization is enabled, false otherwise.
Definition: IsobaricQuantifier.h:71
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:32
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22