| OpenMS 2.5.0

IsobaricIsotopeCorrector.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/Matrix.h>
38 #include <Eigen/Core>
39
40 namespace OpenMS
41 {
42 class IsobaricQuantitationMethod;
43 struct IsobaricQuantifierStatistics;
44 class ConsensusMap;
45 class ConsensusFeature;
46
50 class OPENMS_DLLAPI IsobaricIsotopeCorrector
51 {
52 public:
63 static IsobaricQuantifierStatistics correctIsotopicImpurities(const ConsensusMap& consensus_map_in,
64 ConsensusMap& consensus_map_out,
65 const IsobaricQuantitationMethod* quant_method);
66
67 private:
71 static void fillInputVector_(Eigen::VectorXd& b,
72 Matrix<double>& m_b,
73 const ConsensusFeature& cf,
74 const ConsensusMap& cm);
75
79 static void solveNNLS_(const Matrix<double>& correction_matrix,
80 const Matrix<double>& m_b, Matrix<double>& m_x);
81
85 static void computeStats_(const Matrix<double>& m_x,
86 const Eigen::MatrixXd& x,
87 const float cf_intensity,
88 const IsobaricQuantitationMethod* quant_method,
89 IsobaricQuantifierStatistics& stats);
90
94 static float updateOutpuMap_(const ConsensusMap& consensus_map_in,
95 ConsensusMap& consensus_map_out,
96 Size current_cf,
97 const Matrix<double>& m_x);
98 };
99 } // namespace
100
OpenMS::IsobaricQuantitationMethod
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:54
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
Matrix.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::IsobaricQuantifierStatistics
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...
Definition: IsobaricQuantifierStatistics.h:48
OpenMS::IsobaricIsotopeCorrector
Performs isotope impurity correction on the intensities extracted from an isobaric labeling experimen...
Definition: IsobaricIsotopeCorrector.h:50
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::Matrix< double >
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127