OpenMS  2.5.0
FalseDiscoveryRate.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Andreas Bertsch, Chris Bielow $
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34 
35 #pragma once
36 
42 
43 #include <boost/unordered_map.hpp>
44 
45 #include <vector>
46 #include <unordered_set>
47 
48 namespace OpenMS
49 {
50 
51  struct ScoreToTgtDecLabelPairs;
52 
77  class OPENMS_DLLAPI FalseDiscoveryRate :
78  public DefaultParamHandler
79  {
80 public:
83 
90  void apply(std::vector<PeptideIdentification>& fwd_ids, std::vector<PeptideIdentification>& rev_ids) const;
91 
97  void apply(std::vector<PeptideIdentification>& id) const;
98 
105  void apply(std::vector<ProteinIdentification>& fwd_ids, std::vector<ProteinIdentification>& rev_ids) const;
106 
112  void apply(std::vector<ProteinIdentification>& ids) const;
113 
119  void applyEstimated(std::vector<ProteinIdentification>& ids) const;
120 
130  double applyEvaluateProteinIDs(const std::vector<ProteinIdentification>& ids, double pepCutoff = 1.0, UInt fpCutoff = 50, double diffWeight = 0.2);
131  double applyEvaluateProteinIDs(const ProteinIdentification& ids, double pepCutoff = 1.0, UInt fpCutoff = 50, double diffWeight = 0.2);
132 
134  void applyBasic(std::vector<PeptideIdentification> & ids);
136  void applyBasic(ConsensusMap & cmap, bool use_unassigned_peptides = true);
138  void applyBasic(ProteinIdentification & id, bool groups_too = true);
139 
142  double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff) const;
143 
146  double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff, const String& identifier) const;
147 
150  double rocN(const ConsensusMap& ids, Size fp_cutoff) const;
151 
154  double rocN(const ConsensusMap& ids, Size fp_cutoff, const String& identifier) const;
155 
164  IdentificationData::ScoreTypeRef applyToQueryMatches(IdentificationData& id_data, IdentificationData::ScoreTypeRef score_ref) const;
165 
166 
167 private:
168 
171 
173  FalseDiscoveryRate& operator=(const FalseDiscoveryRate&);
174 
176  void calculateFDRs_(std::map<double, double>& score_to_fdr, std::vector<double>& target_scores, std::vector<double>& decoy_scores, bool q_value, bool higher_score_better) const;
177 
179  void handleQueryMatch_(
182  std::vector<double>& target_scores,
183  std::vector<double>& decoy_scores,
184  std::map<IdentificationData::IdentifiedMoleculeRef, bool>& molecule_to_decoy,
185  std::map<IdentificationData::QueryMatchRef, double>& match_to_score) const;
186 
189  void calculateEstimatedQVal_(std::map<double, double> &scores_to_FDR,
190  ScoreToTgtDecLabelPairs &scores_labels,
191  bool higher_score_better) const;
192 
198  void calculateFDRBasic_(std::map<double,double>& scores_to_FDR, ScoreToTgtDecLabelPairs& scores_labels, bool qvalue, bool higher_score_better) const;
199 
200  //TODO the next two methods could potentially be merged for speed (they iterate over the same structure)
201  //But since they have different cutoff types and it is more generic, I leave it like this.
203  double diffEstimatedEmpirical_(const ScoreToTgtDecLabelPairs& scores_labels, double pepCutoff = 1.0) const;
204 
207  double rocN_(const ScoreToTgtDecLabelPairs& scores_labels, Size fpCutoff = 50) const;
208 
211  double trapezoidal_area_xEqy(double exp1, double exp2, double act1, double act2) const;
212 
214  double trapezoidal_area(double x1, double x2, double y1, double y2) const;
215 
216  };
217 
218 } // namespace OpenMS
219 
Definition: IDScoreGetterSetter.h:53
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:43
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:89
A more convenient string class.
Definition: String.h:58
A container for consensus elements.
Definition: ConsensusMap.h:79
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46