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FeatureFinderIdentificationAlgorithm.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
37
38 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
39 #include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
40 #include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
41 #include <OpenMS/CONCEPT/ProgressLogger.h>
42 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
43 #include <OpenMS/KERNEL/MSExperiment.h>
44 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
45
46 #include <vector>
47 #include <fstream>
48 #include <map>
49
50 namespace OpenMS
51 {
52 class IsotopeDistribution;
53
54
55
56 class OPENMS_DLLAPI FeatureFinderIdentificationAlgorithm :
57 public DefaultParamHandler
58 {
59 public:
61 FeatureFinderIdentificationAlgorithm();
62
66 void run(
67 std::vector<PeptideIdentification> peptides,
68 const std::vector<ProteinIdentification>& proteins,
69 std::vector<PeptideIdentification> peptides_ext,
70 std::vector<ProteinIdentification> proteins_ext,
71 FeatureMap& features,
72 const FeatureMap& seeds = FeatureMap()
73 );
74
75 void runOnCandidates(FeatureMap& features);
76
77 PeakMap& getMSData() { return ms_data_; }
78 const PeakMap& getMSData() const { return ms_data_; }
79
80 PeakMap& getChromatograms() { return chrom_data_; }
81 const PeakMap& getChromatograms() const { return chrom_data_; }
82
83 ProgressLogger& getProgressLogger() { return prog_log_; }
84 const ProgressLogger& getProgressLogger() const { return prog_log_; }
85
86 TargetedExperiment& getLibrary() { return library_; }
87 const TargetedExperiment& getLibrary() const { return library_; }
88
89 protected:
90 typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace;
91 typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces;
92
94 typedef std::multimap<double, PeptideIdentification*> RTMap;
96 typedef std::map<Int, std::pair<RTMap, RTMap> > ChargeMap;
98 typedef std::map<AASequence, ChargeMap> PeptideMap;
100 typedef std::map<String, std::pair<RTMap, RTMap> > PeptideRefRTMap;
101
102 PeptideMap peptide_map_;
103
104 Size n_internal_peps_;
105 Size n_external_peps_;
106
107 Size batch_size_;
108 double rt_window_;
109 double mz_window_;
110 bool mz_window_ppm_;
111
112 double mapping_tolerance_;
113
114 double isotope_pmin_;
115 Size n_isotopes_;
116
117 double rt_quantile_;
118
119 double peak_width_;
120 double min_peak_width_;
121 double signal_to_noise_;
122
123 String elution_model_;
124
125 // SVM related parameters
126 double svm_min_prob_;
127 StringList svm_predictor_names_;
128 String svm_xval_out_;
129 double svm_quality_cutoff;
130 Size svm_n_parts_;
131 Size svm_n_samples_;
132
133 // output file (before filtering)
134 String candidates_out_;
135
136 Size debug_level_;
137
138 void updateMembers_() override;
139
141 struct RTRegion
142 {
143 double start, end;
144 ChargeMap ids;
145 };
146
148 struct FeatureFilterQuality
149 {
150 bool operator()(const Feature& feature)
151 {
152 return feature.getOverallQuality() == 0.0;
153 }
154 } feature_filter_quality_;
155
157 struct FeatureFilterPeptides
158 {
159 bool operator()(const Feature& feature)
160 {
161 return feature.getPeptideIdentifications().empty();
162 }
163 } feature_filter_peptides_;
164
166 struct PeptideCompare
167 {
168 bool operator()(const PeptideIdentification& p1,
169 const PeptideIdentification& p2)
170 {
171 const String& seq1 = p1.getHits()[0].getSequence().toString();
172 const String& seq2 = p2.getHits()[0].getSequence().toString();
173 if (seq1 == seq2)
174 {
175 Int charge1 = p1.getHits()[0].getCharge();
176 Int charge2 = p2.getHits()[0].getCharge();
177 if (charge1 == charge2)
178 {
179 return p1.getRT() < p2.getRT();
180 }
181 return charge1 < charge2;
182 }
183 return seq1 < seq2;
184 }
185 } peptide_compare_;
186
188 struct FeatureCompare
189 {
190 bool operator()(const Feature& f1, const Feature& f2)
191 {
192 const String& ref1 = f1.getMetaValue("PeptideRef");
193 const String& ref2 = f2.getMetaValue("PeptideRef");
194 if (ref1 == ref2)
195 {
196 return f1.getRT() < f2.getRT();
197 }
198 return ref1 < ref2;
199 }
200 } feature_compare_;
201
202 PeakMap ms_data_;
203 PeakMap chrom_data_;
204 TargetedExperiment library_;
205
207 std::map<double, std::pair<Size, Size> > svm_probs_internal_;
209 std::multiset<double> svm_probs_external_;
210 Size n_internal_features_;
211 Size n_external_features_;
212 TransformationDescription trafo_external_;
214 std::map<String, double> isotope_probs_;
215 MRMFeatureFinderScoring feat_finder_;
216
217 ProgressLogger prog_log_;
218
220 void generateTransitions_(const String& peptide_id, double mz, Int charge,
221 const IsotopeDistribution& iso_dist);
222
223 void addPeptideRT_(TargetedExperiment::Peptide& peptide, double rt) const;
224
226 void getRTRegions_(ChargeMap& peptide_data, std::vector<RTRegion>& rt_regions) const;
227
228 void annotateFeaturesFinalizeAssay_(
229 FeatureMap& features,
230 std::map<Size, std::vector<PeptideIdentification*> >& feat_ids,
231 RTMap& rt_internal);
232
234 void annotateFeatures_(FeatureMap& features, PeptideRefRTMap& ref_rt_map);
235
236 void ensureConvexHulls_(Feature& feature);
237
238 void postProcess_(FeatureMap& features, bool with_external_ids);
239
241 void statistics_(const FeatureMap& features) const;
242
245 void createAssayLibrary_(const PeptideMap::iterator& begin, const PeptideMap::iterator& end, PeptideRefRTMap& ref_rt_map);
246
247 void addPeptideToMap_(PeptideIdentification& peptide,
248 PeptideMap& peptide_map,
249 bool external = false) const;
250
251 void checkNumObservations_(Size n_pos, Size n_neg, const String& note = "") const;
252
253 void getUnbiasedSample_(const std::multimap<double, std::pair<Size, bool> >& valid_obs,
254 std::map<Size, Int>& training_labels);
255
256 void getRandomSample_(std::map<Size, Int>& training_labels);
257
258 void classifyFeatures_(FeatureMap& features);
259
260 void filterFeaturesFinalizeAssay_(Feature& best_feature, double best_quality,
261 const double quality_cutoff);
262
263 void filterFeatures_(FeatureMap& features, bool classified);
264
265 void calculateFDR_(FeatureMap& features);
266
269 template <typename It>
270 std::vector<std::pair<It,It>>
271 chunk_(It range_from, It range_to, const std::ptrdiff_t batch_size)
272 {
273 /* Aliases, to make the rest of the code more readable. */
274 using std::vector;
275 using std::pair;
276 using std::make_pair;
277 using std::distance;
278 using diff_t = std::ptrdiff_t;
279
280 /* Total item number and batch_size size. */
281 const diff_t total {distance(range_from, range_to)};
282 const diff_t num {total / batch_size};
283
284 vector<pair<It,It>> chunks(num);
285
286 It batch_end {range_from};
287
288 /* Use the 'generate' algorithm to create batches. */
289 std::generate(begin(chunks), end(chunks), [&batch_end, batch_size]()
290 {
291 It batch_start {batch_end };
292
293 std::advance(batch_end, batch_size);
294 return make_pair(batch_start, batch_end);
295 });
296
297 /* The last batch_size's end must always be 'range_to'. */
298 if (chunks.empty())
299 {
300 chunks.emplace_back(range_from, range_to);
301 }
302 else
303 {
304 chunks.back().second = range_to;
305 }
306
307 return chunks;
308 }
309 };
310
311 } // namespace OpenMS
312
313 #endif
314
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FeatureFinderIdentificationAlgorithm::mapping_tolerance_
double mapping_tolerance_
RT tolerance for mapping IDs to features.
Definition: FeatureFinderIdentificationAlgorithm.h:112
OpenMS::FeatureFinderIdentificationAlgorithm::peptide_map_
PeptideMap peptide_map_
Definition: FeatureFinderIdentificationAlgorithm.h:102
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_features_
Size n_internal_features_
internal feature counter (for FDR calculation)
Definition: FeatureFinderIdentificationAlgorithm.h:210
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:109
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FeatureFinderIdentificationAlgorithm::min_peak_width_
double min_peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:120
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
FeatureFinderAlgorithmPickedHelperStructs.h
OpenMS::Feature::getOverallQuality
QualityType getOverallQuality() const
Non-mutable access to the overall quality.
OpenMS::FeatureFinderIdentificationAlgorithm::svm_n_parts_
Size svm_n_parts_
number of partitions for SVM cross-validation
Definition: FeatureFinderIdentificationAlgorithm.h:130
OpenMS::FeatureFinderIdentificationAlgorithm::signal_to_noise_
double signal_to_noise_
Definition: FeatureFinderIdentificationAlgorithm.h:121
OpenMS::FeatureFinderIdentificationAlgorithm
Definition: FeatureFinderIdentificationAlgorithm.h:56
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::FeatureFinderIdentificationAlgorithm::getMSData
PeakMap & getMSData()
Definition: FeatureFinderIdentificationAlgorithm.h:77
OpenMS::FeatureFinderIdentificationAlgorithm::prog_log_
ProgressLogger prog_log_
Definition: FeatureFinderIdentificationAlgorithm.h:217
TargetedExperiment.h
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::start
double start
Definition: FeatureFinderIdentificationAlgorithm.h:143
OpenMS::FeatureFinderIdentificationAlgorithm::mz_window_
double mz_window_
m/z window width
Definition: FeatureFinderIdentificationAlgorithm.h:109
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::ids
ChargeMap ids
internal/external peptide IDs (per charge) in this region
Definition: FeatureFinderIdentificationAlgorithm.h:144
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureFinderIdentificationAlgorithm::getProgressLogger
const ProgressLogger & getProgressLogger() const
Definition: FeatureFinderIdentificationAlgorithm.h:84
OpenMS::FeatureFinderIdentificationAlgorithm::n_external_features_
Size n_external_features_
Definition: FeatureFinderIdentificationAlgorithm.h:211
OpenMS::FeatureFinderIdentificationAlgorithm::chrom_data_
PeakMap chrom_data_
accumulated chromatograms (XICs)
Definition: FeatureFinderIdentificationAlgorithm.h:203
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality::operator()
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:150
OpenMS::FeatureFinderIdentificationAlgorithm::svm_min_prob_
double svm_min_prob_
Definition: FeatureFinderIdentificationAlgorithm.h:126
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace
Helper struct for mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:79
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare::operator()
bool operator()(const Feature &f1, const Feature &f2)
Definition: FeatureFinderIdentificationAlgorithm.h:190
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideMap
std::map< AASequence, ChargeMap > PeptideMap
mapping: sequence -> charge -> internal/external ID information
Definition: FeatureFinderIdentificationAlgorithm.h:98
OpenMS::FeatureFinderIdentificationAlgorithm::ms_data_
PeakMap ms_data_
input LC-MS data
Definition: FeatureFinderIdentificationAlgorithm.h:202
OpenMS::FeatureFinderIdentificationAlgorithm::peak_width_
double peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:119
OpenMS::FeatureFinderIdentificationAlgorithm::rt_quantile_
double rt_quantile_
Definition: FeatureFinderIdentificationAlgorithm.h:117
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality
predicate for filtering features by overall quality:
Definition: FeatureFinderIdentificationAlgorithm.h:148
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
OpenMS::FeatureFinderIdentificationAlgorithm::candidates_out_
String candidates_out_
Definition: FeatureFinderIdentificationAlgorithm.h:134
MRMFeatureFinderScoring.h
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideRefRTMap
std::map< String, std::pair< RTMap, RTMap > > PeptideRefRTMap
mapping: peptide ref. -> int./ext.: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:100
OpenMS::FeatureFinderIdentificationAlgorithm::getChromatograms
PeakMap & getChromatograms()
Definition: FeatureFinderIdentificationAlgorithm.h:80
OpenMS::FeatureFinderIdentificationAlgorithm::svm_predictor_names_
StringList svm_predictor_names_
Definition: FeatureFinderIdentificationAlgorithm.h:127
ProgressLogger.h
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare
comparison functor for (unassigned) peptide IDs
Definition: FeatureFinderIdentificationAlgorithm.h:166
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FeatureFinderIdentificationAlgorithm::rt_window_
double rt_window_
RT window width.
Definition: FeatureFinderIdentificationAlgorithm.h:108
OpenMS::FeatureFinderIdentificationAlgorithm::getMSData
const PeakMap & getMSData() const
Definition: FeatureFinderIdentificationAlgorithm.h:78
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:207
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
TransformationDescription.h
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_peps_
Size n_internal_peps_
number of internal peptide
Definition: FeatureFinderIdentificationAlgorithm.h:104
DefaultParamHandler.h
OpenMS::FeatureFinderIdentificationAlgorithm::getChromatograms
const PeakMap & getChromatograms() const
Definition: FeatureFinderIdentificationAlgorithm.h:81
OpenMS::FeatureFinderIdentificationAlgorithm::debug_level_
Size debug_level_
Definition: FeatureFinderIdentificationAlgorithm.h:136
OpenMS::FeatureFinderIdentificationAlgorithm::n_isotopes_
Size n_isotopes_
number of isotopes for peptide assay
Definition: FeatureFinderIdentificationAlgorithm.h:115
OpenMS::FeatureFinderIdentificationAlgorithm::elution_model_
String elution_model_
Definition: FeatureFinderIdentificationAlgorithm.h:123
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides
predicate for filtering features by assigned peptides:
Definition: FeatureFinderIdentificationAlgorithm.h:157
OpenMS::FeatureFinderIdentificationAlgorithm::svm_probs_external_
std::multiset< double > svm_probs_external_
SVM probabilities for "external" features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:209
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_pmin_
double isotope_pmin_
min. isotope probability for peptide assay
Definition: FeatureFinderIdentificationAlgorithm.h:114
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides::operator()
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:159
OpenMS::FeatureFinderIdentificationAlgorithm::chunk_
std::vector< std::pair< It, It > > chunk_(It range_from, It range_to, const std::ptrdiff_t batch_size)
Definition: FeatureFinderIdentificationAlgorithm.h:271
int
OpenMS::FeatureFinderIdentificationAlgorithm::MassTrace
FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace
Definition: FeatureFinderIdentificationAlgorithm.h:90
OpenMS::FeatureFinderIdentificationAlgorithm::svm_xval_out_
String svm_xval_out_
Definition: FeatureFinderIdentificationAlgorithm.h:128
OpenMS::FeatureFinderIdentificationAlgorithm::getProgressLogger
ProgressLogger & getProgressLogger()
Definition: FeatureFinderIdentificationAlgorithm.h:83
OpenMS::FeatureFinderIdentificationAlgorithm::svm_n_samples_
Size svm_n_samples_
number of samples for SVM training
Definition: FeatureFinderIdentificationAlgorithm.h:131
OpenMS::FeatureFinderIdentificationAlgorithm::n_external_peps_
Size n_external_peps_
number of external peptides
Definition: FeatureFinderIdentificationAlgorithm.h:105
OpenMS::FeatureFinderIdentificationAlgorithm::library_
TargetedExperiment library_
accumulated assays for peptides
Definition: FeatureFinderIdentificationAlgorithm.h:204
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare
comparison functor for features
Definition: FeatureFinderIdentificationAlgorithm.h:188
OpenMS::FeatureFinderIdentificationAlgorithm::ChargeMap
std::map< Int, std::pair< RTMap, RTMap > > ChargeMap
mapping: charge -> internal/external: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:96
OpenMS::FeatureFinderIdentificationAlgorithm::svm_quality_cutoff
double svm_quality_cutoff
Definition: FeatureFinderIdentificationAlgorithm.h:129
OpenMS::FeatureFinderIdentificationAlgorithm::getLibrary
const TargetedExperiment & getLibrary() const
Definition: FeatureFinderIdentificationAlgorithm.h:87
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion
region in RT in which a peptide elutes:
Definition: FeatureFinderIdentificationAlgorithm.h:141
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()
bool operator()(const PeptideIdentification &p1, const PeptideIdentification &p2)
Definition: FeatureFinderIdentificationAlgorithm.h:168
OpenMS::FeatureFinderIdentificationAlgorithm::RTMap
std::multimap< double, PeptideIdentification * > RTMap
mapping: RT (not necessarily unique) -> pointer to peptide
Definition: FeatureFinderIdentificationAlgorithm.h:94
OpenMS::PeptideIdentification::getRT
double getRT() const
returns the RT of the MS2 spectrum where the identification occurred
OpenMS::FeatureFinderIdentificationAlgorithm::batch_size_
Size batch_size_
nr of peptides to use at the same time during chromatogram extraction
Definition: FeatureFinderIdentificationAlgorithm.h:107
OpenMS::FeatureFinderIdentificationAlgorithm::mz_window_ppm_
bool mz_window_ppm_
m/z window width is given in PPM (not Da)?
Definition: FeatureFinderIdentificationAlgorithm.h:110
OpenMS::FeatureFinderIdentificationAlgorithm::MassTraces
FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces
Definition: FeatureFinderIdentificationAlgorithm.h:91
OpenMS::FeatureFinderIdentificationAlgorithm::getLibrary
TargetedExperiment & getLibrary()
Definition: FeatureFinderIdentificationAlgorithm.h:86
OpenMS::FeatureFinderIdentificationAlgorithm::feat_finder_
MRMFeatureFinderScoring feat_finder_
OpenSWATH feature finder.
Definition: FeatureFinderIdentificationAlgorithm.h:215
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_probs_
std::map< String, double > isotope_probs_
isotope probabilities of transitions
Definition: FeatureFinderIdentificationAlgorithm.h:214