OpenMS  3.0.0
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 
OpenMS::StringUtils::split
static bool split(const String &this_s, const char splitter, std::vector< String > &substrings, bool quote_protect)
Definition: StringUtilsSimple.h:360
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
Size
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
MzMLFile.h
Feature.h
FeatureXMLFile.h
StatisticFunctions.h
OpenMS::Peak2D::getIntensity
IntensityType getIntensity() const
Definition: Peak2D.h:166
Constants.h
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MRMRTNormalizer
The MRMRTNormalizer will find retention time peptides in data.
Definition: MRMRTNormalizer.h:57
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::Peak2D::getMZ
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
TOPPBase.h
OpenMS::Math::absdev
static double absdev(IteratorType begin, IteratorType end, double mean=std::numeric_limits< double >::max())
Calculates the absolute deviation of a range of values.
Definition: StatisticFunctions.h:336
OpenMS::ConsensusFeature::insert
void insert(const ConsensusFeature &cf)
Adds all feature handles (of the CF) into the consensus feature.
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58