| OpenMS 2.5.0

Classes | Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | List of all members
ConfidenceScoring Class Reference

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

Inheritance diagram for ConfidenceScoring:

## Classes

struct | GLM_
| Binomial GLM. More...
struct | RTNorm_
| Helper for RT normalization (range 0-100) More...

## Public Member Functions

| ConfidenceScoring (bool test_mode_=false)
| Constructor. More...
virtual | ~ConfidenceScoring ()
void | initialize (const TargetedExperiment &library, const Size n_decoys, const Size n_transitions, const 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...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) 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)
| 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 OpenMS::ConfidenceScoring::GLM_ | glm_
struct OpenMS::ConfidenceScoring::RTNorm_ | rt_norm_
TargetedExperiment | library_
| assay library More...
IntList | decoy_index_
| indexes of assays to use as decoys More...
Size | n_decoys_
| number of decoys to use (per feature/true assay) More...
Map< String, IntList > | transition_map_
| assay (ID) -> transitions (indexes) More...
Size | n_transitions_
| number of transitions to consider More...
TransformationDescription | rt_trafo_
| RT transformation to map measured RTs to assay RTs. More...
boost::mt19937 | generator_
| random number generation engine More...
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

typedef boost::bimap<double, boost::bimaps::multiset_of<double> > BimapType

protected

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

## Constructor & Destructor Documentation

## ◆ ConfidenceScoring()

ConfidenceScoring | ( | bool | test_mode_ = `false` | ) |

inline explicit

Constructor.

## ◆ ~ConfidenceScoring()

virtual ~ConfidenceScoring | ( |  | ) |

inline virtual

## Member Function Documentation

## ◆ chooseDecoys_()

void chooseDecoys_ | ( |  | ) |

protected

Randomize the list of decoy indexes.

## ◆ extractIntensities_()

void extractIntensities_ | ( | BimapType & | intensity_map,
|  | Size | n_transitions,
|  | DoubleList & | intensities
| ) |  |

protected

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

## ◆ getAssayRT_()

double getAssayRT_ | ( | const TargetedExperiment::Peptide & | assay | ) |

protected

Get the retention time of an assay.

## ◆ initialize()

void initialize | ( | const TargetedExperiment & | library,
|  | const Size | n_decoys,
|  | const Size | n_transitions,
|  | const TransformationDescription & | rt_trafo
| ) |  |

inline

## ◆ initializeGlm()

void initializeGlm | ( | double | intercept,
|  | double | rt_coef,
|  | double | int_coef
| ) |  |

inline

## ◆ manhattanDist_()

double manhattanDist_ | ( | DoubleList | x,
|  | DoubleList | y
| ) |  |

protected

Manhattan distance.

## ◆ scoreAssay_()

double scoreAssay_ | ( | const TargetedExperiment::Peptide & | assay,
|  | double | 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`)

## ◆ scoreFeature_()

void scoreFeature_ | ( | Feature & | feature | ) |

protected

Score a feature.

## ◆ scoreMap()

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 TargetedExperiment::getPeptides(), TargetedExperiment::getTransitions(), UniqueIdInterface::getUniqueId(), OPENMS_LOG_DEBUG, and OPENMS_LOG_WARN.

## Member Data Documentation

## ◆ decoy_index_

IntList decoy_index_

protected

indexes of assays to use as decoys

## ◆ generator_

boost::mt19937 generator_

protected

random number generation engine

## ◆ glm_

struct OpenMS::ConfidenceScoring::GLM_ glm_

protected

## ◆ library_

TargetedExperiment library_

protected

assay library

## ◆ n_decoys_

Size n_decoys_

protected

number of decoys to use (per feature/true assay)

## ◆ n_transitions_

Size n_transitions_

protected

number of transitions to consider

## ◆ rand_gen_

boost::variate_generator<boost::mt19937&, boost::uniform_int<> > rand_gen_

protected

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

## ◆ rt_norm_

struct OpenMS::ConfidenceScoring::RTNorm_ rt_norm_

protected

## ◆ rt_trafo_

TransformationDescription rt_trafo_

protected

RT transformation to map measured RTs to assay RTs.

## ◆ transition_map_

Map<String, IntList> transition_map_

protected

assay (ID) -> transitions (indexes)