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ConfidenceScoring Class Reference

#include <OpenMS/ANALYSIS/OPENSWATH/ConfidenceScoring.h>

Inheritance diagram for ConfidenceScoring:
ProgressLogger

Public Member Functions

 ConfidenceScoring (bool test_mode_=false)
 Constructor. More...
 
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...
 
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
< DoubleReal,
boost::bimaps::multiset_of
< DoubleReal > > 
BimapType
 Mapping: Q3 m/z <-> transition intensity (maybe not unique!) More...
 

Protected Member Functions

void chooseDecoys_ ()
 Randomize the list of decoy indexes. More...
 
DoubleReal manhattanDist_ (DoubleList x, DoubleList y)
 Manhattan distance. More...
 
DoubleReal 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)
 
DoubleReal scoreAssay_ (const TargetedExperiment::Peptide &assay, DoubleReal 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 {
   DoubleReal   intercept
 
   DoubleReal   rt_coef
 
   DoubleReal   int_coef
 
glm_
 Binomial GLM. More...
 
struct {
   DoubleReal   min_rt
 
   DoubleReal   max_rt
 
rt_norm_
 Helper for RT normalization (range 0-100) More...
 
TargetedExperiment library_
 
IntList decoy_index_
 
Size n_decoys_
 
Map< String, IntListtransition_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_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Member Typedef Documentation

typedef boost::bimap<DoubleReal, boost::bimaps::multiset_of<DoubleReal> > BimapType
protected

Mapping: Q3 m/z <-> transition intensity (maybe not unique!)

Constructor & Destructor Documentation

ConfidenceScoring ( bool  test_mode_ = false)
inline

Constructor.

Member Function Documentation

void chooseDecoys_ ( )
protected

Randomize the list of decoy indexes.

void extractIntensities_ ( BimapType intensity_map,
Size  n_transitions,
DoubleList intensities 
)
protected

Extract the n_transitions highest intensities from intensity_map, store them in intensities

DoubleReal getAssayRT_ ( const TargetedExperiment::Peptide assay,
const String cv_accession = "MS:1000896" 
)
protected

Get the retention time of an assay.

void initialize ( TargetedExperiment  library,
Size  n_decoys,
Size  n_transitions,
TransformationDescription  rt_trafo 
)
inline
void initializeGlm ( double  intercept,
double  rt_coef,
double  int_coef 
)
inline
DoubleReal manhattanDist_ ( DoubleList  x,
DoubleList  y 
)
protected

Manhattan distance.

DoubleReal scoreAssay_ ( const TargetedExperiment::Peptide assay,
DoubleReal  feature_rt,
DoubleList feature_intensities,
const std::set< String > &  transition_ids = std::set< String >() 
)
protected

Score the assay assay against feature data (feature_rt, feature_intensities), optionally using only the specified transitions (transition_ids)

void scoreFeature_ ( Feature feature)
protected

Score a feature.

void scoreMap ( FeatureMap<> &  features)
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 UniqueIdInterface::getUniqueId(), LOG_DEBUG, and LOG_WARN.

Member Data Documentation

IntList decoy_index_
protected
boost::mt19937 generator_
protected
struct { ... } glm_

Binomial GLM.

DoubleReal int_coef
DoubleReal intercept
TargetedExperiment library_
protected
DoubleReal max_rt
DoubleReal min_rt
Size n_decoys_
protected
Size n_transitions_
protected
boost::variate_generator<boost::mt19937&, boost::uniform_int<> > rand_gen_
protected

Random number generator (must be initialized in init. list of c'tor!)

DoubleReal rt_coef
struct { ... } rt_norm_

Helper for RT normalization (range 0-100)

TransformationDescription rt_trafo_
protected

RT transformation to map measured RTs to assay RTs.

Map<String, IntList> transition_map_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5