OpenMS  2.6.0
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  double applyEvaluateProteinIDs(ScoreToTgtDecLabelPairs& score_to_tgt_dec_fraction_pairs, double pepCutoff = 1.0, UInt fpCutoff = 50, double diffWeight = 0.2);
133 
135  void applyBasic(std::vector<PeptideIdentification> & ids);
137  void applyBasic(ConsensusMap & cmap, bool use_unassigned_peptides = true);
139  void applyBasic(ProteinIdentification & id, bool groups_too = true);
140 
143  double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff) const;
144 
147  double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff, const String& identifier) const;
148 
151  double rocN(const ConsensusMap& ids, Size fp_cutoff) const;
152 
155  double rocN(const ConsensusMap& ids, Size fp_cutoff, const String& identifier) const;
156 
157  //TODO the next two methods could potentially be merged for speed (they iterate over the same structure)
158  //But since they have different cutoff types and it is more generic, I leave it like this.
160  double diffEstimatedEmpirical(const ScoreToTgtDecLabelPairs& scores_labels, double pepCutoff = 1.0) const;
161 
164  double rocN(const ScoreToTgtDecLabelPairs& scores_labels, Size fpCutoff = 50) const;
165 
174  IdentificationData::ScoreTypeRef applyToQueryMatches(IdentificationData& id_data, IdentificationData::ScoreTypeRef score_ref) const;
175 
176 
177 private:
178 
181 
183  FalseDiscoveryRate& operator=(const FalseDiscoveryRate&);
184 
186  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;
187 
189  void handleQueryMatch_(
192  std::vector<double>& target_scores,
193  std::vector<double>& decoy_scores,
194  std::map<IdentificationData::IdentifiedMoleculeRef, bool>& molecule_to_decoy,
195  std::map<IdentificationData::QueryMatchRef, double>& match_to_score) const;
196 
199  void calculateEstimatedQVal_(std::map<double, double> &scores_to_FDR,
200  ScoreToTgtDecLabelPairs &scores_labels,
201  bool higher_score_better) const;
202 
208  void calculateFDRBasic_(std::map<double,double>& scores_to_FDR, ScoreToTgtDecLabelPairs& scores_labels, bool qvalue, bool higher_score_better) const;
209 
212  double trapezoidal_area_xEqy(double exp1, double exp2, double act1, double act2) const;
213 
215  double trapezoidal_area(double x1, double x2, double y1, double y2) const;
216 
217  };
218 
219 } // namespace OpenMS
220 
DefaultParamHandler.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
OpenMS::Param::copy
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
FileHandler.h
FileTypes.h
OpenMS::FalseDiscoveryRate::apply
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.
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::String
A more convenient string class.
Definition: String.h:59
ConsensusMap.h
OpenMS::IDFilter::updateProteinReferences
static void updateProteinReferences(std::vector< PeptideIdentification > &peptides, const std::vector< ProteinIdentification > &proteins, bool remove_peptides_without_reference=false)
Removes references to missing proteins.
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::IDFilter::updateProteinGroups
static bool updateProteinGroups(std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &hits)
Update protein groups after protein hits were filtered.
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OPENMS_LOG_FATAL_ERROR
#define OPENMS_LOG_FATAL_ERROR
Macro to be used if fatal error are reported (processing stops)
Definition: LogStream.h:450
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::IDFilter::removeUnreferencedProteins
static void removeUnreferencedProteins(ConsensusMap &cmap, bool include_unassigned)
OpenMS::IdentificationDataInternal::IteratorWrapper
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:43
ProteinIdentification.h
OpenMS::IDFilter::updateHitRanks
static void updateHitRanks(std::vector< IdentificationType > &ids)
Updates the hit ranks on all peptide or protein IDs.
Definition: IDFilter.h:740
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::IDFilter::countHits
static Size countHits(const std::vector< IdentificationType > &ids)
Returns the total number of peptide/protein hits in a vector of peptide/protein identifications.
Definition: IDFilter.h:613
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:80
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::FalseDiscoveryRate
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::IdentificationData
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:89
OpenMS::ScoreToTgtDecLabelPairs
Definition: IDScoreGetterSetter.h:53
OpenMS::IDFilter::removeEmptyIdentifications
static void removeEmptyIdentifications(std::vector< IdentificationType > &ids)
Removes peptide or protein identifications that have no hits in them.
Definition: IDFilter.h:810
OpenMS::Exception::BaseException::getMessage
const char * getMessage() const noexcept
Returns the message.
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::FalseDiscoveryRate::applyBasic
void applyBasic(std::vector< PeptideIdentification > &ids)
simpler reimplemetation of the apply function above.
IdentificationData.h
IDFilter.h
OpenMS::IDFilter::filterHitsByScore
static void filterHitsByScore(std::vector< IdentificationType > &ids, double threshold_score)
Filters peptide or protein identifications according to the score of the hits.
Definition: IDFilter.h:822
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:195
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
PeptideIdentification.h
FalseDiscoveryRate.h
StandardTypes.h
TOPPBase.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63