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MRMRTNormalizer.h
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger, Hannes Roest $
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMRTNORMALIZER_H
36 #define OPENMS_ANALYSIS_OPENSWATH_MRMRTNORMALIZER_H
37 
38 #include <OpenMS/config.h>
39 
40 #include <cstddef> // for size_t & ptrdiff_t
41 #include <vector>
42 #include <string>
43 
44 namespace OpenMS
45 {
46 
58  class OPENMS_DLLAPI MRMRTNormalizer
59  {
60 
61 private:
62 
69  static double llsm_rsq(std::vector<std::pair<double, double> >& pairs);
70 
71  static std::pair<double, double > llsm_fit(std::vector<std::pair<double, double> >& pairs);
72 
75  static double llsm_rss(std::vector<std::pair<double, double> >& pairs, std::pair<double, double >& coefficients);
76 
79  static std::vector<std::pair<double, double> > llsm_rss_inliers(std::vector<std::pair<double, double> >& pairs,
80  std::pair<double, double >& coefficients, double max_threshold);
81 
93  static int jackknifeOutlierCandidate(std::vector<double>& x, std::vector<double>& y);
94 
106  static int residualOutlierCandidate(std::vector<double>& x, std::vector<double>& y);
107 
108 public:
109 
135  static std::vector<std::pair<double, double> > removeOutliersRANSAC(std::vector<std::pair<double, double> >& pairs,
136  double rsq_limit,
137  double coverage_limit,
138  size_t max_iterations,
139  double max_rt_threshold,
140  size_t sampling_size);
141 
158  static std::vector<std::pair<double, double> > ransac(std::vector<std::pair<double, double> >& pairs, size_t n, size_t k, double t, size_t d, bool test = false);
159 
186  static std::vector<std::pair<double, double> > removeOutliersIterative(std::vector<std::pair<double, double> >& pairs,
187  double rsq_limit,
188  double coverage_limit,
189  bool use_chauvenet,
190  std::string method);
191 
198  static double chauvenet_probability(std::vector<double>& residuals, int pos);
199 
206  static bool chauvenet(std::vector<double>& residuals, int pos);
207  };
208 
209 }
210 #endif
const double k
The MRMRTNormalizer will find retention time peptides in data.
Definition: MRMRTNormalizer.h:58
bool test
Status of the current subsection.

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:40 using doxygen 1.8.5