35 #ifndef OPENMS_ANALYSIS_OPENSWATH_CONFIDENCESCORING
36 #define OPENMS_ANALYSIS_OPENSWATH_CONFIDENCESCORING
41 #include <boost/bimap.hpp>
42 #include <boost/bimap/multiset_of.hpp>
43 #include <boost/random/uniform_int.hpp>
44 #include <boost/random/mersenne_twister.hpp>
45 #include <boost/random/variate_generator.hpp>
65 generator_(), rand_gen_(generator_, boost::uniform_int<>())
67 if (!test_mode_) rand_gen_.engine().seed(time(0));
73 typedef boost::bimap<DoubleReal, boost::bimaps::multiset_of<DoubleReal> >
85 DoubleReal lm = intercept + rt_coef * diff_rt * diff_rt +
87 return 1.0 / (1.0 + exp(-lm));
99 return (rt - min_rt) / (max_rt - min_rt) * 100;
119 boost::variate_generator<boost::mt19937&, boost::uniform_int<> >
rand_gen_;
122 void chooseDecoys_();
129 const String& cv_accession =
"MS:1000896");
133 void extractIntensities_(
BimapType& intensity_map,
Size n_transitions,
141 const std::set<String>& transition_ids = std::set<String>());
144 void scoreFeature_(
Feature& feature);
151 n_decoys_ = n_decoys;
152 n_transitions_ = n_transitions;
153 rt_trafo_ = rt_trafo;
158 glm_.intercept = intercept;
159 glm_.rt_coef = rt_coef;
160 glm_.int_coef = int_coef;
178 Size n_assays = library_.getPeptides().size();
182 "There need to be at least 2 assays in the library for ConfidenceScoring.");
185 if (n_assays - 1 < n_decoys_)
187 LOG_WARN <<
"Warning: Parameter 'decoys' (" << n_decoys_
188 <<
") is higher than the number of unrelated assays in the "
189 <<
"library (" << n_assays - 1 <<
"). "
190 <<
"Using all unrelated assays as decoys." << std::endl;
192 if (n_assays - 1 <= n_decoys_) n_decoys_ = 0;
194 decoy_index_.resize(n_assays);
195 for (
Size i = 0; i < n_assays; ++i) decoy_index_[i] = boost::numeric_cast<Int>(i);
198 LOG_DEBUG <<
"Building transition map..." << std::endl;
199 for (
Size i = 0; i < library_.getTransitions().size(); ++i)
201 const String& ref = library_.getTransitions()[i].getPeptideRef();
202 transition_map_[ref].push_back(boost::numeric_cast<Int>(i));
205 LOG_DEBUG <<
"Determining retention time range..." << std::endl;
206 rt_norm_.min_rt = std::numeric_limits<double>::infinity();
207 rt_norm_.max_rt = -std::numeric_limits<double>::infinity();
208 for (std::vector<TargetedExperiment::Peptide>::const_iterator it =
209 library_.getPeptides().begin(); it != library_.getPeptides().end();
213 if (current_rt == -1.0)
continue;
214 rt_norm_.min_rt = std::min(rt_norm_.min_rt, current_rt);
215 rt_norm_.max_rt = std::max(rt_norm_.max_rt, current_rt);
219 LOG_DEBUG <<
"Scoring features..." << std::endl;
220 startProgress(0, features.size(),
"scoring features");
223 feat_it != features.end(); ++feat_it)
225 LOG_DEBUG <<
"Feature " << feat_it - features.begin() + 1
226 <<
" (ID '" << feat_it->
getUniqueId() <<
"')"<< std::endl;
227 scoreFeature_(*feat_it);
228 setProgress(feat_it - features.begin());
238 #endif // OPENMS_ANALYSIS_OPENSWATH_CONFIDENCESCORING
DoubleReal rt_coef
Definition: ConfidenceScoring.h:80
A more convenient string class.
Definition: String.h:56
void initializeGlm(double intercept, double rt_coef, double int_coef)
Definition: ConfidenceScoring.h:156
DoubleReal min_rt
Definition: ConfidenceScoring.h:94
DoubleReal int_coef
Definition: ConfidenceScoring.h:81
void scoreMap(FeatureMap<> &features)
Score a feature map -> make sure the class is properly initialized.
Definition: ConfidenceScoring.h:175
Map< String, IntList > transition_map_
Definition: ConfidenceScoring.h:109
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:459
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged...
Definition: LogStream.h:451
TargetedExperiment library_
Definition: ConfidenceScoring.h:103
TransformationDescription rt_trafo_
RT transformation to map measured RTs to assay RTs.
Definition: ConfidenceScoring.h:114
boost::mt19937 generator_
Definition: ConfidenceScoring.h:116
DoubleReal max_rt
Definition: ConfidenceScoring.h:95
A method or algorithm argument contains illegal values.
Definition: Exception.h:634
ConfidenceScoring(bool test_mode_=false)
Constructor.
Definition: ConfidenceScoring.h:64
DoubleReal intercept
Definition: ConfidenceScoring.h:79
IntList decoy_index_
Definition: ConfidenceScoring.h:105
An LC-MS feature.
Definition: Feature.h:66
void initialize(TargetedExperiment library, Size n_decoys, Size n_transitions, TransformationDescription rt_trafo)
Definition: ConfidenceScoring.h:148
Definition: ConfidenceScoring.h:58
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Size n_decoys_
Definition: ConfidenceScoring.h:107
Size n_transitions_
Definition: ConfidenceScoring.h:111
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
boost::variate_generator< boost::mt19937 &, boost::uniform_int<> > rand_gen_
Random number generator (must be initialized in init. list of c'tor!)
Definition: ConfidenceScoring.h:119
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:109
DoubleReal list.
Definition: DoubleList.h:56
boost::bimap< DoubleReal, boost::bimaps::multiset_of< DoubleReal > > BimapType
Mapping: Q3 m/z <-> transition intensity (maybe not unique!)
Definition: ConfidenceScoring.h:74
Definition: TargetedExperimentHelper.h:211
Int list.
Definition: IntList.h:56