Calculates a consensus ID from several ID runs. More...
#include <OpenMS/ANALYSIS/ID/ConsensusID.h>
Inheritance diagram for ConsensusID:
Public Member Functions | |
| ConsensusID () | |
| Default constructor. | |
| void | apply (std::vector< PeptideIdentification > &ids) |
| Calculates the consensus ID for a set of PeptideIdentification instances of the same spectrum. | |
Private Member Functions | |
| ConsensusID (const ConsensusID &) | |
| Not implemented. | |
| ConsensusID & | operator= (const ConsensusID &) |
| Not implemented. | |
| void | ranked_ (std::vector< PeptideIdentification > &ids) |
| Ranked algorithm. | |
| void | average_ (std::vector< PeptideIdentification > &ids) |
| Average score algorithm. | |
| void | PEPMatrix_ (std::vector< PeptideIdentification > &ids) |
| PEP and scoring matrix based algorithm. | |
| void | PEPIons_ (std::vector< PeptideIdentification > &ids) |
| PEP and ion similarity based algorithm. | |
| void | Minimum_ (std::vector< PeptideIdentification > &ids) |
| use minimal PEP score | |
| void | mapIdentifications_ (std::vector< PeptideIdentification > &sorted_ids, const std::vector< PeptideIdentification > &ids) |
| Merge peptide hits from different engines. | |
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:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| 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 |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
| ConsensusID | ( | ) |
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 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |