Calculates a consensus ID from several ID runs. More...
#include <OpenMS/ANALYSIS/ID/ConsensusID.h>
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... | |
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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 DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () 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... | |
ConsensusID & | operator= (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 | |
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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... | |
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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< String > | subsections_ |
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... | |
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:Name | Type | Default | Restrictions | Description |
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algorithm | string | PEPMatrix | ranked, average, PEPMatrix, PEPIons, Minimum | Algorithm 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 | int | 10 | min: 1 | The number of top hits that are used for the consensus scoring. |
number_of_runs | int | 0 | min: 0 | The 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 | int | 2 | min: 0 | The minimal number of similar (between two suggested sequences) fragment ion masses that is necessary to evaluate the shared peak count similarity (SPC). |
PEPIons:common | float | 1.1 | min: 0 max: 1.1 | Similarity 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 | float | 1.1 | min: 0 max: 1.1 | Similarity 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 | int | 5 | Give the gap penalty (the same penalty will be used for opening and extension) as a positive integer |
ConsensusID | ( | ) |
Default constructor.
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private |
Not implemented.
void apply | ( | std::vector< PeptideIdentification > & | ids | ) |
Calculates the consensus ID for a set of PeptideIdentification instances of the same spectrum.
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private |
Average score algorithm.
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private |
Merge peptide hits from different engines.
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private |
use minimal PEP score
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private |
Not implemented.
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private |
PEP and ion similarity based algorithm.
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private |
PEP and scoring matrix based algorithm.
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private |
Ranked algorithm.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |