OpenMS  2.4.0
FeatureFinderIdentificationAlgorithm.h
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34 
35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
37 
45 
46 #include <vector>
47 #include <fstream>
48 #include <map>
49 
50 namespace OpenMS
51 {
52  class IsotopeDistribution;
53 
55  public DefaultParamHandler
56 {
57 public:
60 
64  void run(
65  std::vector<PeptideIdentification> peptides,
66  std::vector<ProteinIdentification> proteins,
67  std::vector<PeptideIdentification> peptides_ext,
68  std::vector<ProteinIdentification> proteins_ext,
69  FeatureMap& features
70  );
71 
72  void runOnCandidates(FeatureMap& features);
73 
74  PeakMap& getMSData() { return ms_data_; }
75  const PeakMap& getMSData() const { return ms_data_; }
76 
77  PeakMap& getChromatograms() { return chrom_data_; }
78  const PeakMap& getChromatograms() const { return chrom_data_; }
79 
80  ProgressLogger& getProgressLogger() { return prog_log_; }
81  const ProgressLogger& getProgressLogger() const { return prog_log_; }
82 
83  TargetedExperiment& getLibrary() { return library_; }
84  const TargetedExperiment& getLibrary() const { return library_; }
85 
86 protected:
89 
91  typedef std::multimap<double, PeptideIdentification*> RTMap;
93  typedef std::map<Int, std::pair<RTMap, RTMap> > ChargeMap;
95  typedef std::map<AASequence, ChargeMap> PeptideMap;
97  typedef std::map<String, std::pair<RTMap, RTMap> > PeptideRefRTMap;
98 
100 
101  Size n_internal_peps_; //< number of internal peptide
102  Size n_external_peps_; //< number of external peptides
103 
104  double rt_window_; //< RT window width
105  double mz_window_; //< m/z window width
106  bool mz_window_ppm_; //< m/z window width is given in PPM (not Da)?
107 
108  double mapping_tolerance_; //< RT tolerance for mapping IDs to features
109 
110  double isotope_pmin_; //< min. isotope probability for peptide assay
111  Size n_isotopes_; //< number of isotopes for peptide assay
112 
113  double rt_quantile_;
114 
115  double peak_width_;
118 
120 
121  // SVM related parameters
126  Size svm_n_parts_; //< number of partitions for SVM cross-validation
127  Size svm_n_samples_; //< number of samples for SVM training
128 
129  // output file (before filtering)
131 
133 
134  void updateMembers_() override;
135 
137  struct RTRegion
138  {
139  double start, end;
140  ChargeMap ids; //< internal/external peptide IDs (per charge) in this region
141  };
142 
145  {
146  bool operator()(const Feature& feature)
147  {
148  return feature.getOverallQuality() == 0.0;
149  }
150  } feature_filter_quality_;
151 
154  {
155  bool operator()(const Feature& feature)
156  {
157  return feature.getPeptideIdentifications().empty();
158  }
159  } feature_filter_peptides_;
160 
163  {
165  const PeptideIdentification& p2)
166  {
167  const String& seq1 = p1.getHits()[0].getSequence().toString();
168  const String& seq2 = p2.getHits()[0].getSequence().toString();
169  if (seq1 == seq2)
170  {
171  Int charge1 = p1.getHits()[0].getCharge();
172  Int charge2 = p2.getHits()[0].getCharge();
173  if (charge1 == charge2)
174  {
175  return p1.getRT() < p2.getRT();
176  }
177  return charge1 < charge2;
178  }
179  return seq1 < seq2;
180  }
181  } peptide_compare_;
182 
185  {
186  bool operator()(const Feature& f1, const Feature& f2)
187  {
188  const String& ref1 = f1.getMetaValue("PeptideRef");
189  const String& ref2 = f2.getMetaValue("PeptideRef");
190  if (ref1 == ref2)
191  {
192  return f1.getRT() < f2.getRT();
193  }
194  return ref1 < ref2;
195  }
196  } feature_compare_;
197 
198  PeakMap ms_data_; //< input LC-MS data
199  PeakMap chrom_data_; //< accumulated chromatograms (XICs)
200  TargetedExperiment library_; //< accumulated assays for peptides
201 
203  std::map<double, std::pair<Size, Size> > svm_probs_internal_;
205  std::multiset<double> svm_probs_external_;
206  Size n_internal_features_; //< internal feature counter (for FDR calculation)
207  Size n_external_features_; //< external feature counter (for FDR calculation)
209  TransformationDescription trafo_external_; //< transform. to external RT scale
210  std::map<String, double> isotope_probs_; //< isotope probabilities of transitions
211  MRMFeatureFinderScoring feat_finder_; //< OpenSWATH feature finder
212 
214 
216  void generateTransitions_(const String& peptide_id, double mz, Int charge,
217  const IsotopeDistribution& iso_dist);
218 
219  void addPeptideRT_(TargetedExperiment::Peptide& peptide, double rt) const;
220 
222  void getRTRegions_(ChargeMap& peptide_data, std::vector<RTRegion>& rt_regions) const;
223 
224  void annotateFeaturesFinalizeAssay_(
225  FeatureMap& features,
226  std::map<Size, std::vector<PeptideIdentification*> >& feat_ids,
227  RTMap& rt_internal);
228 
230  void annotateFeatures_(FeatureMap& features, PeptideRefRTMap& ref_rt_map);
231 
232  void ensureConvexHulls_(Feature& feature);
233 
234  void postProcess_(FeatureMap& features, bool with_external_ids);
235 
237  void statistics_(const FeatureMap& features) const;
238 
239  void createAssayLibrary_(PeptideMap& peptide_map, PeptideRefRTMap& ref_rt_map);
240 
241  void addPeptideToMap_(PeptideIdentification& peptide,
242  PeptideMap& peptide_map,
243  bool external = false) const;
244 
245  void checkNumObservations_(Size n_pos, Size n_neg, const String& note = "") const;
246 
247  void getUnbiasedSample_(const std::multimap<double, std::pair<Size, bool> >& valid_obs,
248  std::map<Size, Int>& training_labels);
249 
250  void getRandomSample_(std::map<Size, Int>& training_labels);
251 
252  void classifyFeatures_(FeatureMap& features);
253 
254  void filterFeaturesFinalizeAssay_(Feature& best_feature, double best_quality,
255  const double quality_cutoff);
256 
257  void filterFeatures_(FeatureMap& features, bool classified);
258 
259  void calculateFDR_(FeatureMap& features);
260 
261  };
262 
263 } // namespace OpenMS
264 
265 #endif
266 
DefaultParamHandler.h
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare::operator()
bool operator()(const Feature &f1, const Feature &f2)
Definition: FeatureFinderIdentificationAlgorithm.h:186
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::start
double start
Definition: FeatureFinderIdentificationAlgorithm.h:139
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
TargetedExperiment.h
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideMap
std::map< AASequence, ChargeMap > PeptideMap
mapping: sequence -> charge -> internal/external ID information
Definition: FeatureFinderIdentificationAlgorithm.h:95
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides::operator()
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:155
OpenMS::TraMLFile::store
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
OpenMS::FeatureFinderIdentificationAlgorithm::ms_data_
PeakMap ms_data_
Definition: FeatureFinderIdentificationAlgorithm.h:198
OpenMS::FeatureFinderIdentificationAlgorithm::feat_finder_
MRMFeatureFinderScoring feat_finder_
Definition: FeatureFinderIdentificationAlgorithm.h:211
OpenMS::FeatureFinderIdentificationAlgorithm::getChromatograms
PeakMap & getChromatograms()
Definition: FeatureFinderIdentificationAlgorithm.h:77
OpenMS::FeatureFinderIdentificationAlgorithm::svm_n_parts_
Size svm_n_parts_
Definition: FeatureFinderIdentificationAlgorithm.h:126
OpenMS::FeatureFinderIdentificationAlgorithm::getLibrary
const TargetedExperiment & getLibrary() const
Definition: FeatureFinderIdentificationAlgorithm.h:84
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_pmin_
double isotope_pmin_
Definition: FeatureFinderIdentificationAlgorithm.h:110
OpenMS::FeatureFinderIdentificationAlgorithm::peptide_map_
PeptideMap peptide_map_
Definition: FeatureFinderIdentificationAlgorithm.h:99
OpenMS::FeatureFinderIdentificationAlgorithm::getMSData
PeakMap & getMSData()
Definition: FeatureFinderIdentificationAlgorithm.h:74
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:451
TransformationModel.h
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
OpenMS::Feature::getOverallQuality
QualityType getOverallQuality() const
Non-mutable access to the overall quality.
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::FeatureFinderIdentificationAlgorithm::peak_width_
double peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:115
OpenMS::FeatureFinderIdentificationAlgorithm::getProgressLogger
ProgressLogger & getProgressLogger()
Definition: FeatureFinderIdentificationAlgorithm.h:80
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_probs_
std::map< String, double > isotope_probs_
Definition: FeatureFinderIdentificationAlgorithm.h:210
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace
Helper struct for mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:79
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare
comparison functor for features
Definition: FeatureFinderIdentificationAlgorithm.h:184
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
FeatureXMLFile.h
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::ids
ChargeMap ids
Definition: FeatureFinderIdentificationAlgorithm.h:140
OpenMS::FeatureFinderIdentificationAlgorithm::getProgressLogger
const ProgressLogger & getProgressLogger() const
Definition: FeatureFinderIdentificationAlgorithm.h:81
OpenMS::FeatureFinderIdentificationAlgorithm::signal_to_noise_
double signal_to_noise_
Definition: FeatureFinderIdentificationAlgorithm.h:117
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()
bool operator()(const PeptideIdentification &p1, const PeptideIdentification &p2)
Definition: FeatureFinderIdentificationAlgorithm.h:164
FeatureFinderAlgorithmPickedHelperStructs.h
TransformationDescription.h
OpenMS::FeatureFinderIdentificationAlgorithm::candidates_out_
String candidates_out_
Definition: FeatureFinderIdentificationAlgorithm.h:130
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
OpenMS::FeatureFinderIdentificationAlgorithm::svm_probs_external_
std::multiset< double > svm_probs_external_
SVM probabilities for "external" features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:205
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name) const
Returns the value corresponding to a string (or DataValue::EMPTY if not found)
OpenMS::FeatureFinderIdentificationAlgorithm::library_
TargetedExperiment library_
Definition: FeatureFinderIdentificationAlgorithm.h:200
OpenMS::FeatureFinderIdentificationAlgorithm::MassTrace
FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace
Definition: FeatureFinderIdentificationAlgorithm.h:87
OpenMS::FeatureFinderIdentificationAlgorithm::getLibrary
TargetedExperiment & getLibrary()
Definition: FeatureFinderIdentificationAlgorithm.h:83
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::FeatureFinderIdentificationAlgorithm
Definition: FeatureFinderIdentificationAlgorithm.h:54
OpenMS::FeatureFinderIdentificationAlgorithm::n_external_peps_
Size n_external_peps_
Definition: FeatureFinderIdentificationAlgorithm.h:102
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality
predicate for filtering features by overall quality:
Definition: FeatureFinderIdentificationAlgorithm.h:144
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::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::FeatureFinderIdentificationAlgorithm::svm_n_samples_
Size svm_n_samples_
Definition: FeatureFinderIdentificationAlgorithm.h:127
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FeatureFinderIdentificationAlgorithm::ChargeMap
std::map< Int, std::pair< RTMap, RTMap > > ChargeMap
mapping: charge -> internal/external: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:93
OpenMS::TraMLFile
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
IsotopeDistribution.h
ProgressLogger.h
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides
predicate for filtering features by assigned peptides:
Definition: FeatureFinderIdentificationAlgorithm.h:153
OpenMS::FeatureFinderIdentificationAlgorithm::svm_min_prob_
double svm_min_prob_
Definition: FeatureFinderIdentificationAlgorithm.h:122
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
MRMFeatureFinderScoring.h
TransformationXMLFile.h
OpenMS::FeatureFinderIdentificationAlgorithm::mz_window_
double mz_window_
Definition: FeatureFinderIdentificationAlgorithm.h:105
CoarseIsotopePatternGenerator.h
OpenMS::FeatureFinderIdentificationAlgorithm::svm_quality_cutoff
double svm_quality_cutoff
Definition: FeatureFinderIdentificationAlgorithm.h:125
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
OpenMS::FeatureFinderIdentificationAlgorithm::debug_level_
Size debug_level_
Definition: FeatureFinderIdentificationAlgorithm.h:132
MapAlignmentAlgorithmIdentification.h
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideRefRTMap
std::map< String, std::pair< RTMap, RTMap > > PeptideRefRTMap
mapping: peptide ref. -> int./ext.: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:97
OpenMS::FeatureFinderIdentificationAlgorithm::mapping_tolerance_
double mapping_tolerance_
Definition: FeatureFinderIdentificationAlgorithm.h:108
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::FeatureFinderIdentificationAlgorithm::svm_predictor_names_
StringList svm_predictor_names_
Definition: FeatureFinderIdentificationAlgorithm.h:123
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion
region in RT in which a peptide elutes:
Definition: FeatureFinderIdentificationAlgorithm.h:137
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality::operator()
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:146
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
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
OpenMS::FeatureFinderIdentificationAlgorithm::getChromatograms
const PeakMap & getChromatograms() const
Definition: FeatureFinderIdentificationAlgorithm.h:78
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
MSExperiment.h
OpenMS::FeatureFinderIdentificationAlgorithm::RTMap
std::multimap< double, PeptideIdentification * > RTMap
mapping: RT (not necessarily unique) -> pointer to peptide
Definition: FeatureFinderIdentificationAlgorithm.h:91
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:72
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FeatureFinderIdentificationAlgorithm::run
void run(std::vector< PeptideIdentification > peptides, std::vector< ProteinIdentification > proteins, std::vector< PeptideIdentification > peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features)
OpenMS::FeatureFinderIdentificationAlgorithm::n_isotopes_
Size n_isotopes_
Definition: FeatureFinderIdentificationAlgorithm.h:111
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare
comparison functor for (unassigned) peptide IDs
Definition: FeatureFinderIdentificationAlgorithm.h:162
OpenMS::FeatureFinderIdentificationAlgorithm::trafo_external_
TransformationDescription trafo_external_
TransformationDescription trafo_; // RT transformation (to range 0-1)
Definition: FeatureFinderIdentificationAlgorithm.h:209
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_features_
Size n_internal_features_
Definition: FeatureFinderIdentificationAlgorithm.h:206
OpenMS::FeatureFinderIdentificationAlgorithm::rt_quantile_
double rt_quantile_
Definition: FeatureFinderIdentificationAlgorithm.h:113
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::DataProcessing::QUANTITATION
@ QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
OpenMS::FeatureFinderIdentificationAlgorithm::MassTraces
FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces
Definition: FeatureFinderIdentificationAlgorithm.h:88
OpenMS::FeatureFinderIdentificationAlgorithm::getMSData
const PeakMap & getMSData() const
Definition: FeatureFinderIdentificationAlgorithm.h:75
OpenMS::FeatureFinderIdentificationAlgorithm::min_peak_width_
double min_peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:116
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::FeatureFinderIdentificationAlgorithm::rt_window_
double rt_window_
Definition: FeatureFinderIdentificationAlgorithm.h:104
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:109
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS::FeatureFinderIdentificationAlgorithm::mz_window_ppm_
bool mz_window_ppm_
Definition: FeatureFinderIdentificationAlgorithm.h:106
OpenMS::FeatureFinderIdentificationAlgorithm::n_external_features_
Size n_external_features_
Definition: FeatureFinderIdentificationAlgorithm.h:207
OpenMS::FeatureFinderIdentificationAlgorithm::svm_probs_internal_
std::map< double, std::pair< Size, Size > > svm_probs_internal_
SVM probability -> number of pos./neg. features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:203
OpenMS::FeatureFinderIdentificationAlgorithm::chrom_data_
PeakMap chrom_data_
Definition: FeatureFinderIdentificationAlgorithm.h:199
OpenMS::FeatureFinderIdentificationAlgorithm::runOnCandidates
void runOnCandidates(FeatureMap &features)
OpenMS::DataProcessing::FILTERING
@ FILTERING
Data filtering or extraction.
Definition: DataProcessing.h:71
TraMLFile.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:60
FeatureFinderIdentificationAlgorithm.h
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_peps_
Size n_internal_peps_
Definition: FeatureFinderIdentificationAlgorithm.h:101
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::FeatureFinderIdentificationAlgorithm::prog_log_
ProgressLogger prog_log_
Definition: FeatureFinderIdentificationAlgorithm.h:213
OpenMS::FeatureFinderIdentificationAlgorithm::elution_model_
String elution_model_
Definition: FeatureFinderIdentificationAlgorithm.h:119
MSSpectrum.h
OpenMS::FeatureFinderIdentificationAlgorithm::svm_xval_out_
String svm_xval_out_
Definition: FeatureFinderIdentificationAlgorithm.h:124
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS::PeptideIdentification::getRT
double getRT() const
returns the RT of the MS2 spectrum where the identification occurred