| OpenMS 2.5.0

MRMRTNormalizer.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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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
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MRMRTNormalizer
The MRMRTNormalizer will find retention time peptides in data.
Definition: MRMRTNormalizer.h:57