Calculates an FDR from identifications. More...
#include <OpenMS/ANALYSIS/ID/FalseDiscoveryRate.h>
Public Member Functions | |
| FalseDiscoveryRate () | |
| Default constructor. | |
| void | apply (std::vector< PeptideIdentification > &fwd_ids, std::vector< PeptideIdentification > &rev_ids) |
| Calculates the FDR of two runs, a forward run and a decoy run on peptide level. | |
| void | apply (std::vector< PeptideIdentification > &id) |
| Calculates the FDR of one run from a concatenated sequence db search. | |
| void | apply (std::vector< ProteinIdentification > &fwd_ids, std::vector< ProteinIdentification > &rev_ids) |
| Calculates the FDR of two runs, a forward run and decoy run on protein level. | |
| void | apply (std::vector< ProteinIdentification > &ids) |
| Calculate the FDR of one run from a concatenated sequence db search. | |
Private Member Functions | |
| FalseDiscoveryRate (const FalseDiscoveryRate &) | |
| Not implemented. | |
| FalseDiscoveryRate & | operator= (const FalseDiscoveryRate &) |
| Not implemented. | |
| void | calculateFDRs_ (Map< DoubleReal, DoubleReal > &score_to_fdr, std::vector< DoubleReal > &target_scores, std::vector< DoubleReal > &decoy_scores, bool q_value, bool higher_score_better) |
| calculates the fdr stored into fdrs, given two vectors of scores | |
Detailed Description
Calculates an FDR from identifications.
Either two runs of forward and decoy database identification or one run containing both (with marks) can be used to annotate each of the peptide hits with a FDR.
Also q-values can be reported instead of p-values. q-values are basically only adjusted p-values, also ranging from 0 to 1, with lower values being preferable. When looking at the list of hits ordered by q-values, then a hit with q-value of x means that there is an x*100 percent chance that all hits with a q-value <= x are a false positive hit.
- Todo:
- implement combined searches properly (Andreas)
- Improvement:
- implement charge state separated fdr/q-values (Andreas)
| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| q_value | string | true | true, false | If 'true', the q-values will be calculated instead of the FDRs |
| use_all_hits | string | false | true, false | If 'true' not only the first hit, but all are used (peptides only) |
| split_charge_variants | string | false | true, false | If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only). |
| treat_runs_separately | string | false | true, false | If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only). |
| decoy_string | string | _rev | String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only). | |
| add_decoy_peptides | string | false | true, false | If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
Default constructor.
| FalseDiscoveryRate | ( | const FalseDiscoveryRate & | ) | [private] |
Not implemented.
Member Function Documentation
| void apply | ( | std::vector< PeptideIdentification > & | fwd_ids, | |
| std::vector< PeptideIdentification > & | rev_ids | |||
| ) |
Calculates the FDR of two runs, a forward run and a decoy run on peptide level.
- Parameters:
-
fwd_ids forward peptide identifications rev_ids reverse peptide identifications
Referenced by IDEvaluationBase::getPoints().
| void apply | ( | std::vector< PeptideIdentification > & | id | ) |
Calculates the FDR of one run from a concatenated sequence db search.
- Parameters:
-
id peptide identifications, containing target and decoy hits
| void apply | ( | std::vector< ProteinIdentification > & | ids | ) |
Calculate the FDR of one run from a concatenated sequence db search.
- Parameters:
-
ids protein identifications, containing target and decoy hits
| void apply | ( | std::vector< ProteinIdentification > & | fwd_ids, | |
| std::vector< ProteinIdentification > & | rev_ids | |||
| ) |
Calculates the FDR of two runs, a forward run and decoy run on protein level.
- Parameters:
-
fwd_ids forward protein identifications rev_ids reverse protein identifications
| void calculateFDRs_ | ( | Map< DoubleReal, DoubleReal > & | score_to_fdr, | |
| std::vector< DoubleReal > & | target_scores, | |||
| std::vector< DoubleReal > & | decoy_scores, | |||
| bool | q_value, | |||
| bool | higher_score_better | |||
| ) | [private] |
calculates the fdr stored into fdrs, given two vectors of scores
| FalseDiscoveryRate& operator= | ( | const FalseDiscoveryRate & | ) | [private] |
Not implemented.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |