OpenMS  2.8.0
FalseDiscoveryRate.h
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32 // $Authors: Andreas Bertsch, Chris Bielow $
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34 
35 #pragma once
36 
42 
43 #include <unordered_map>
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) const;
140  double applyEvaluateProteinIDs(const ProteinIdentification& ids, double pepCutoff = 1.0, UInt fpCutoff = 50, double diffWeight = 0.2) const;
141 
151  double applyEvaluateProteinIDs(ScoreToTgtDecLabelPairs& score_to_tgt_dec_fraction_pairs, double pepCutoff = 1.0, UInt fpCutoff = 50, double diffWeight = 0.2) const;
152 
154  void applyBasic(std::vector<PeptideIdentification> & ids);
156  void applyBasic(ConsensusMap & cmap, bool use_unassigned_peptides = true);
158  void applyBasic(ProteinIdentification & id, bool groups_too = true);
159 
169  void applyPickedProteinFDR(ProteinIdentification& id, String decoy_string = "", bool prefix = true, bool groups_too = true);
170 
173  double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff) const;
174 
177  double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff, const String& identifier) const;
178 
181  double rocN(const ConsensusMap& ids, Size fp_cutoff) const;
182 
185  double rocN(const ConsensusMap& ids, Size fp_cutoff, const String& identifier) const;
186 
187  //TODO the next two methods could potentially be merged for speed (they iterate over the same structure)
188  //But since they have different cutoff types and it is more generic, I leave it like this.
190  double diffEstimatedEmpirical(const ScoreToTgtDecLabelPairs& scores_labels, double pepCutoff = 1.0) const;
191 
194  double rocN(const ScoreToTgtDecLabelPairs& scores_labels, Size fpCutoff = 50) const;
195 
205 
210  {
211  public:
215  struct Result
216  {
217  bool success;
219  bool is_prefix;
220  };
221 
229  };
230 private:
231 
234 
237 
239  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;
240 
245  std::vector<double>& target_scores,
246  std::vector<double>& decoy_scores,
247  std::map<IdentificationData::IdentifiedMolecule, bool>& molecule_to_decoy,
248  std::map<IdentificationData::ObservationMatchRef, double>& match_to_score) const;
249 
252  void calculateEstimatedQVal_(std::map<double, double> &scores_to_FDR,
253  ScoreToTgtDecLabelPairs &scores_labels,
254  bool higher_score_better) const;
255 
261  void calculateFDRBasic_(std::map<double,double>& scores_to_FDR, ScoreToTgtDecLabelPairs& scores_labels, bool qvalue, bool higher_score_better) const;
262 
265  double trapezoidal_area_xEqy(double exp1, double exp2, double act1, double act2) const;
266 
268  double trapezoidal_area(double x1, double x2, double y1, double y2) const;
269  };
270 
271 } // namespace OpenMS
A container for consensus elements.
Definition: ConsensusMap.h:90
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
Finds decoy strings in ProteinIdentification runs.
Definition: FalseDiscoveryRate.h:210
bool is_prefix
on success, was it a prefix or suffix
Definition: FalseDiscoveryRate.h:219
bool success
did more than 30% of proteins have the *same* prefix or suffix
Definition: FalseDiscoveryRate.h:217
static Result findDecoyString(const ProteinIdentification &proteins)
String name
on success, what was the decoy string?
Definition: FalseDiscoveryRate.h:218
Finds the most common decoy string in the accessions of proteins. Checks for suffix and prefix and so...
Definition: FalseDiscoveryRate.h:216
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:79
void applyBasic(ConsensusMap &cmap, bool use_unassigned_peptides=true)
simpler reimplementation of the apply function above for peptides in ConsensusMaps.
double applyEvaluateProteinIDs(const std::vector< ProteinIdentification > &ids, double pepCutoff=1.0, UInt fpCutoff=50, double diffWeight=0.2) const
Calculate a linear combination of the area of the difference in estimated vs. empirical (TD) FDR and ...
void apply(std::vector< PeptideIdentification > &id) const
Calculates the FDR of one run from a concatenated sequence DB search.
FalseDiscoveryRate & operator=(const FalseDiscoveryRate &)
Not implemented.
void apply(std::vector< PeptideIdentification > &fwd_ids, std::vector< PeptideIdentification > &rev_ids) const
Calculates the FDR of two runs, a forward run and a decoy run on peptide level.
double rocN(const std::vector< PeptideIdentification > &ids, Size fp_cutoff) const
double rocN(const ConsensusMap &ids, Size fp_cutoff, const String &identifier) const
void applyPickedProteinFDR(ProteinIdentification &id, String decoy_string="", bool prefix=true, bool groups_too=true)
Applies a picked protein FDR. Behaves like a normal target-decoy FDR where only the score of the best...
double rocN(const ConsensusMap &ids, Size fp_cutoff) const
void applyBasic(std::vector< PeptideIdentification > &ids)
simpler reimplementation of the apply function above.
void apply(std::vector< ProteinIdentification > &fwd_ids, std::vector< ProteinIdentification > &rev_ids) const
Calculates the FDR of two runs, a forward run and decoy run on protein level.
FalseDiscoveryRate()
Default constructor.
double diffEstimatedEmpirical(const ScoreToTgtDecLabelPairs &scores_labels, double pepCutoff=1.0) const
calculates the area of the difference between estimated and empirical FDR on the fly....
void applyEstimated(std::vector< ProteinIdentification > &ids) const
Calculate the FDR based on PEPs or PPs (if present) and modifies the IDs inplace.
IdentificationData::ScoreTypeRef applyToObservationMatches(IdentificationData &id_data, IdentificationData::ScoreTypeRef score_ref) const
Calculate FDR on the level of observation matches (e.g. peptide-spectrum matches) for "general" ident...
void calculateFDRBasic_(std::map< double, double > &scores_to_FDR, ScoreToTgtDecLabelPairs &scores_labels, bool qvalue, bool higher_score_better) const
FalseDiscoveryRate(const FalseDiscoveryRate &)
Not implemented.
double applyEvaluateProteinIDs(ScoreToTgtDecLabelPairs &score_to_tgt_dec_fraction_pairs, double pepCutoff=1.0, UInt fpCutoff=50, double diffWeight=0.2) const
Calculate a linear combination of the area of the difference in estimated vs. empirical (TD) FDR and ...
void apply(std::vector< ProteinIdentification > &ids) const
Calculate the FDR of one run from a concatenated sequence db search.
double rocN(const std::vector< PeptideIdentification > &ids, Size fp_cutoff, const String &identifier) const
double trapezoidal_area_xEqy(double exp1, double exp2, double act1, double act2) const
void handleObservationMatch_(IdentificationData::ObservationMatchRef match_ref, IdentificationData::ScoreTypeRef score_ref, std::vector< double > &target_scores, std::vector< double > &decoy_scores, std::map< IdentificationData::IdentifiedMolecule, bool > &molecule_to_decoy, std::map< IdentificationData::ObservationMatchRef, double > &match_to_score) const
Helper function for applyToObservationMatches()
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
calculates the FDR, given two vectors of scores
double trapezoidal_area(double x1, double x2, double y1, double y2) const
calculates the trapezoidal area for a trapezoid with a flat horizontal base e.g. for an AUC
void applyBasic(ProteinIdentification &id, bool groups_too=true)
simpler reimplementation of the apply function above for proteins.
double applyEvaluateProteinIDs(const ProteinIdentification &ids, double pepCutoff=1.0, UInt fpCutoff=50, double diffWeight=0.2) const
Calculate a linear combination of the area of the difference in estimated vs. empirical (TD) FDR and ...
double rocN(const ScoreToTgtDecLabelPairs &scores_labels, Size fpCutoff=50) const
void calculateEstimatedQVal_(std::map< double, double > &scores_to_FDR, ScoreToTgtDecLabelPairs &scores_labels, bool higher_score_better) const
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:95
Representation of a protein identification run.
Definition: ProteinIdentification.h:72
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static String prefix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:147
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:46
Definition: IDScoreGetterSetter.h:57