OpenMS  2.8.0
MRMRTNormalizer.h
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger, Hannes Roest $
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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:47