OpenMS
MRMRTNormalizer.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 2002-2023.
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: George Rosenberger $
32 // $Authors: George Rosenberger, Hannes Roest $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
38 
39 #include <cstddef> // for size_t & ptrdiff_t
40 #include <vector>
41 #include <string>
42 
43 namespace OpenMS
44 {
45 
57  class OPENMS_DLLAPI MRMRTNormalizer
58  {
59 
60 protected:
61 
73  static int jackknifeOutlierCandidate_(const std::vector<double>& x, const std::vector<double>& y);
74 
86  static int residualOutlierCandidate_(const std::vector<double>& x, const std::vector<double>& y);
87 
88 public:
89 
115  static std::vector<std::pair<double, double> > removeOutliersRANSAC(const std::vector<std::pair<double, double> >& pairs,
116  double rsq_limit,
117  double coverage_limit,
118  size_t max_iterations,
119  double max_rt_threshold,
120  size_t sampling_size);
121 
148  static std::vector<std::pair<double, double> > removeOutliersIterative(const std::vector<std::pair<double, double> >& pairs,
149  double rsq_limit,
150  double coverage_limit,
151  bool use_chauvenet,
152  const std::string& method);
153 
160  static double chauvenet_probability(const std::vector<double>& residuals, int pos);
161 
168  static bool chauvenet(const std::vector<double>& residuals, int pos);
169 
182  static bool computeBinnedCoverage(const std::pair<double,double> & rtRange,
183  const std::vector<std::pair<double, double> > & pairs,
184  int nrBins,
185  int minPeptidesPerBin,
186  int minBinsFilled);
187 
188  };
189 
190 }
191 
The MRMRTNormalizer will find retention time peptides in data.
Definition: MRMRTNormalizer.h:58
static std::vector< std::pair< double, double > > removeOutliersIterative(const std::vector< std::pair< double, double > > &pairs, double rsq_limit, double coverage_limit, bool use_chauvenet, const std::string &method)
This function removes potential outliers in a linear regression dataset.
static bool chauvenet(const std::vector< double > &residuals, int pos)
This function computes Chauvenet's criterion for a vector and a value whose position is submitted.
static int residualOutlierCandidate_(const std::vector< double > &x, const std::vector< double > &y)
This function computes a candidate outlier peptide by computing the residuals of all points to the li...
static int jackknifeOutlierCandidate_(const std::vector< double > &x, const std::vector< double > &y)
This function computes a candidate outlier peptide by iteratively leaving one peptide out to find the...
static std::vector< std::pair< double, double > > removeOutliersRANSAC(const std::vector< std::pair< double, double > > &pairs, double rsq_limit, double coverage_limit, size_t max_iterations, double max_rt_threshold, size_t sampling_size)
This function removes potential outliers in a linear regression dataset.
static bool computeBinnedCoverage(const std::pair< double, double > &rtRange, const std::vector< std::pair< double, double > > &pairs, int nrBins, int minPeptidesPerBin, int minBinsFilled)
Computes coverage of the RT normalization peptides over the whole RT range, ensuring that each bin ha...
static double chauvenet_probability(const std::vector< double > &residuals, int pos)
This function computes Chauvenet's criterion probability for a vector and a value whose position is s...
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48