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ConsensusID Class Reference

Calculates a consensus ID from several ID runs. More...

#include <OpenMS/ANALYSIS/ID/ConsensusID.h>

Inheritance diagram for ConsensusID:
DefaultParamHandler

Public Member Functions

 ConsensusID ()
 Default constructor. More...
 
void apply (std::vector< PeptideIdentification > &ids)
 Calculates the consensus ID for a set of PeptideIdentification instances of the same spectrum. More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Private Member Functions

 ConsensusID (const ConsensusID &)
 Not implemented. More...
 
ConsensusIDoperator= (const ConsensusID &)
 Not implemented. More...
 
void ranked_ (std::vector< PeptideIdentification > &ids)
 Ranked algorithm. More...
 
void average_ (std::vector< PeptideIdentification > &ids)
 Average score algorithm. More...
 
void PEPMatrix_ (std::vector< PeptideIdentification > &ids)
 PEP and scoring matrix based algorithm. More...
 
void PEPIons_ (std::vector< PeptideIdentification > &ids)
 PEP and ion similarity based algorithm. More...
 
void Minimum_ (std::vector< PeptideIdentification > &ids)
 use minimal PEP score More...
 
void mapIdentifications_ (std::vector< PeptideIdentification > &sorted_ids, const std::vector< PeptideIdentification > &ids)
 Merge peptide hits from different engines. More...
 

Additional Inherited Members

- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

Calculates a consensus ID from several ID runs.

This class combines several ID runs using one of several, available algorithms.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
algorithm stringPEPMatrix ranked, average, PEPMatrix, PEPIons, MinimumAlgorithm used for the consensus scoring.
ranked -- reorders the hits according to a consensus score computed from the ranks in the input runs. The score is normalized to the interval (0,100). The PeptideIdentifications do not need to have the same score type.
average -- reorders the hits according to the average score of the input runs. Make sure to use PeptideIdentifications with the same score type only!
PEPMatrix -- calculates a consensus score based on posterior error probabilities and scoring matrices for siimilarity. This algorithm uses the PAM30MS matrix to score sequences not listed by all engines. Make sure to use PeptideIdentifications with score types converted to PEPs only!
PEPIons -- calculates a consensus score based on posterior error probabilities and fragment ion siimilarity. Make sure to use PeptideIdentifications with score types converted to PEPs only!
Minimum -- calculates a consensus score based on the minimal score. Make sure to use PeptideIdentifications with score types converted to PEPs only!
considered_hits int10 min: 1The number of top hits that are used for the consensus scoring.
number_of_runs int0 min: 0The number of runs used as input. This information is used in 'Ranked' and 'Average' to compute the new scores. If not given, the number of input identifications is taken.
PEPIons:MinNumberOfFragments int2 min: 0The minimal number of similar (between two suggested sequences) fragment ion masses that is necessary to evaluate the shared peak count similarity (SPC).
PEPIons:common float1.1 min: 0 max: 1.1Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -> pep 1 with score x1 and engine2 -> pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 >= common, Note that 0 <= degree of similarity <= 1. Values > 1 will disable this option.
PEPMatrix:common float1.1 min: 0 max: 1.1Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -> pep 1 with score x1 and engine2 -> pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 >= common, Note that 0 <= degree of similarity <= 1. Values > 1 will disable this option.
PEPMatrix:penalty int5  Give the gap penalty (the same penalty will be used for opening and extension) as a positive integer

Note:

Constructor & Destructor Documentation

Default constructor.

ConsensusID ( const ConsensusID )
private

Not implemented.

Member Function Documentation

void apply ( std::vector< PeptideIdentification > &  ids)

Calculates the consensus ID for a set of PeptideIdentification instances of the same spectrum.

Note
Make sure that the score orientation (PeptideIdentification::isHigherScoreBetter())is set properly!
void average_ ( std::vector< PeptideIdentification > &  ids)
private

Average score algorithm.

void mapIdentifications_ ( std::vector< PeptideIdentification > &  sorted_ids,
const std::vector< PeptideIdentification > &  ids 
)
private

Merge peptide hits from different engines.

void Minimum_ ( std::vector< PeptideIdentification > &  ids)
private

use minimal PEP score

ConsensusID& operator= ( const ConsensusID )
private

Not implemented.

void PEPIons_ ( std::vector< PeptideIdentification > &  ids)
private

PEP and ion similarity based algorithm.

void PEPMatrix_ ( std::vector< PeptideIdentification > &  ids)
private

PEP and scoring matrix based algorithm.

void ranked_ ( std::vector< PeptideIdentification > &  ids)
private

Ranked algorithm.


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:44 using doxygen 1.8.5