#include <OpenMS/ANALYSIS/OPENSWATH/ConfidenceScoring.h>
Inheritance diagram for ConfidenceScoring:
Public Member Functions | |
| ConfidenceScoring (bool test_mode_=false) | |
| Constructor. More... | |
| virtual | ~ConfidenceScoring () |
| void | initialize (TargetedExperiment library, Size n_decoys, Size n_transitions, TransformationDescription rt_trafo) |
| void | initializeGlm (double intercept, double rt_coef, double int_coef) |
| void | scoreMap (FeatureMap &features) |
| Score a feature map -> make sure the class is properly initialized. More... | |
 Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| ~ProgressLogger () | |
| Destructor. More... | |
| ProgressLogger (const ProgressLogger &other) | |
| Copy constructor. More... | |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress () const |
| Ends the progress display. More... | |
Protected Types | |
| typedef boost::bimap< double, boost::bimaps::multiset_of< double > > | BimapType |
| Mapping: Q3 m/z <-> transition intensity (maybe not unique!) More... | |
Protected Member Functions | |
| void | chooseDecoys_ () |
| Randomize the list of decoy indexes. More... | |
| double | manhattanDist_ (DoubleList x, DoubleList y) |
| Manhattan distance. More... | |
| double | getAssayRT_ (const TargetedExperiment::Peptide &assay, const String &cv_accession="MS:1000896") |
| Get the retention time of an assay. More... | |
| void | extractIntensities_ (BimapType &intensity_map, Size n_transitions, DoubleList &intensities) |
| double | scoreAssay_ (const TargetedExperiment::Peptide &assay, double feature_rt, DoubleList &feature_intensities, const std::set< String > &transition_ids=std::set< String >()) |
| void | scoreFeature_ (Feature &feature) |
| Score a feature. More... | |
Protected Attributes | |
| struct { | |
| double intercept | |
| double rt_coef | |
| double int_coef | |
| } | glm_ |
| Binomial GLM. More... | |
| struct { | |
| double min_rt | |
| double max_rt | |
| } | rt_norm_ |
| Helper for RT normalization (range 0-100) More... | |
| TargetedExperiment | library_ |
| IntList | decoy_index_ |
| Size | n_decoys_ |
| Map< String, IntList > | transition_map_ |
| Size | n_transitions_ |
| TransformationDescription | rt_trafo_ |
| RT transformation to map measured RTs to assay RTs. More... | |
| boost::mt19937 | generator_ |
| boost::variate_generator< boost::mt19937 &, boost::uniform_int<> > | rand_gen_ |
| Random number generator (must be initialized in init. list of c'tor!) More... | |
| Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| time_t | last_invoke_ |
| ProgressLoggerImpl * | current_logger_ |
Additional Inherited Members | |
| Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. More... | |
| Static Protected Member Functions inherited from ProgressLogger | |
| static String | logTypeToFactoryName_ (LogType type) |
| Return the name of the factory product used for this log type. More... | |
| Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
Member Typedef Documentation
◆ BimapType
Mapping: Q3 m/z <-> transition intensity (maybe not unique!)
Constructor & Destructor Documentation
◆ ConfidenceScoring()
|
inlineexplicit |
Constructor.
◆ ~ConfidenceScoring()
|
inlinevirtual |
Member Function Documentation
◆ chooseDecoys_()
|
protected |
Randomize the list of decoy indexes.
◆ extractIntensities_()
|
protected |
Extract the n_transitions highest intensities from intensity_map, store them in intensities
◆ getAssayRT_()
|
protected |
Get the retention time of an assay.
◆ initialize()
|
inline |
◆ initializeGlm()
◆ manhattanDist_()
|
protected |
Manhattan distance.
◆ scoreAssay_()
|
protected |
Score the assay assay against feature data (feature_rt, feature_intensities), optionally using only the specified transitions (transition_ids)
◆ scoreFeature_()
|
protected |
Score a feature.
◆ scoreMap()
|
inline |
Score a feature map -> make sure the class is properly initialized.
both functions initializeGlm and initialize need to be called first.
The input to the program is
- a transition library which contains peptides with corresponding assays.
- a feature map where each feature corresponds to an assay (mapped with MetaValue "PeptideRef") and each feature has as many subordinates as the assay has transitions (mapped with MetaValue "native_id").
References TargetedExperiment::getPeptides(), TargetedExperiment::getTransitions(), UniqueIdInterface::getUniqueId(), LOG_DEBUG, and LOG_WARN.
Member Data Documentation
◆ decoy_index_
|
protected |
◆ generator_
|
protected |
◆ glm_
| struct { ... } glm_ |
Binomial GLM.
◆ int_coef
| double int_coef |
◆ intercept
| double intercept |
◆ library_
|
protected |
◆ max_rt
| double max_rt |
◆ min_rt
| double min_rt |
◆ n_decoys_
|
protected |
◆ n_transitions_
|
protected |
◆ rand_gen_
|
protected |
Random number generator (must be initialized in init. list of c'tor!)
◆ rt_coef
| double rt_coef |
◆ rt_norm_
| struct { ... } rt_norm_ |
Helper for RT normalization (range 0-100)
◆ rt_trafo_
|
protected |
RT transformation to map measured RTs to assay RTs.