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| FalseDiscoveryRate () |
| Default constructor. More...
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void | apply (std::vector< PeptideIdentification > &fwd_ids, std::vector< PeptideIdentification > &rev_ids) const |
| Calculates the FDR of two runs, a forward run and a decoy run on peptide level. More...
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void | apply (std::vector< PeptideIdentification > &id) const |
| Calculates the FDR of one run from a concatenated sequence DB search. More...
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void | apply (std::vector< ProteinIdentification > &fwd_ids, std::vector< ProteinIdentification > &rev_ids) const |
| Calculates the FDR of two runs, a forward run and decoy run on protein level. More...
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void | apply (std::vector< ProteinIdentification > &ids) const |
| Calculate the FDR of one run from a concatenated sequence db search. More...
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void | applyEstimated (std::vector< ProteinIdentification > &ids) const |
| Calculate the FDR based on PEPs or PPs (if present) and modifies the IDs inplace. More...
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double | applyEvaluateProteinIDs (const std::vector< ProteinIdentification > &ids, double pepCutoff=1.0, UInt fpCutoff=50, double diffWeight=0.2) |
| Calculate a linear combination of the area of the difference in estimated vs. empirical (TD) FDR and the ROC-N value (AUC up to first N false positives). More...
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double | applyEvaluateProteinIDs (const ProteinIdentification &ids, double pepCutoff=1.0, UInt fpCutoff=50, double diffWeight=0.2) |
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void | applyBasic (std::vector< PeptideIdentification > &ids) |
| simpler reimplemetation of the apply function above. More...
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void | applyBasic (ConsensusMap &cmap, bool use_unassigned_peptides=true) |
| simpler reimplemetation of the apply function above for peptides in ConsensusMaps. More...
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void | applyBasic (ProteinIdentification &id, bool groups_too=true) |
| simpler reimplemetation of the apply function above for proteins. More...
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double | rocN (const std::vector< PeptideIdentification > &ids, Size fp_cutoff) const |
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double | rocN (const std::vector< PeptideIdentification > &ids, Size fp_cutoff, const String &identifier) const |
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double | rocN (const ConsensusMap &ids, Size fp_cutoff) const |
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double | rocN (const ConsensusMap &ids, Size fp_cutoff, const String &identifier) const |
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IdentificationData::ScoreTypeRef | applyToQueryMatches (IdentificationData &id_data, IdentificationData::ScoreTypeRef score_ref) const |
| Calculate FDR on the level of molecule-query matches (e.g. peptide-spectrum matches) for "general" identification data. More...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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| FalseDiscoveryRate (const FalseDiscoveryRate &) |
| Not implemented. More...
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FalseDiscoveryRate & | operator= (const FalseDiscoveryRate &) |
| Not implemented. More...
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void | calculateFDRs_ (std::map< double, double > &score_to_fdr, std::vector< double > &target_scores, std::vector< double > &decoy_scores, bool q_value, bool higher_score_better) const |
| calculates the FDR, given two vectors of scores More...
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void | handleQueryMatch_ (IdentificationData::QueryMatchRef match_ref, IdentificationData::ScoreTypeRef score_ref, std::vector< double > &target_scores, std::vector< double > &decoy_scores, std::map< IdentificationData::IdentifiedMoleculeRef, bool > &molecule_to_decoy, std::map< IdentificationData::QueryMatchRef, double > &match_to_score) const |
| Helper function for applyToQueryMatches() More...
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void | calculateEstimatedQVal_ (std::map< double, double > &scores_to_FDR, ScoreToTgtDecLabelPairs &scores_labels, bool higher_score_better) const |
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void | calculateFDRBasic_ (std::map< double, double > &scores_to_FDR, ScoreToTgtDecLabelPairs &scores_labels, bool qvalue, bool higher_score_better) const |
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double | diffEstimatedEmpirical_ (const ScoreToTgtDecLabelPairs &scores_labels, double pepCutoff=1.0) const |
| calculates the area of the difference between estimated and empirical FDR on the fly. Does not store results. More...
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double | rocN_ (const ScoreToTgtDecLabelPairs &scores_labels, Size fpCutoff=50) const |
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double | trapezoidal_area_xEqy (double exp1, double exp2, double act1, double act2) const |
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double | trapezoidal_area (double x1, double x2, double y1, double y2) const |
| calculates the trapezoidal area for a trapezoid with a flat horizontal base e.g. for an AUC More...
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Calculates false discovery rates (FDR) from identifications.
Either two runs of forward and decoy database identification or one run containing both (with annotations) can be used to annotate each of the peptide hits with an FDR or q-value.
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 specific q-value of x means that x*100 percent of hits with a q-value <= x are expected to be false positives.
Only simple target-decoy FDRs are supported with a formula depending on the "conservative" parameter:
- false: (D+1)/T.
- true: (D+1)/(T+D) [for comparison with protein level FDR in Fido mostly] For protein groups, a group is considered as a target when it contains at least one target protein. Group level FDRs assume the same score type as on protein level.
For peptide hits, a hit is considered target also if it maps to both a target and a decoy protein (i.e. "target+decoy") as value in the "target_decoy" metavalue e.g. annotated by PeptideIndexer
- Note
- The parameter add_decoy_proteins currently does not affect groups
Parameters of this class are:
Name | Type | Default | Restrictions | Description |
no_qvalues |
string | false |
true, false | If 'true' strict FDRs will be calculated instead of q-values (the default) |
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 'true' charge variants are treated separately (for peptides of combined target/decoy searches only). |
treat_runs_separately |
string | false |
true, false | If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only). |
add_decoy_peptides |
string | false |
true, false | If 'true' decoy peptides will be written to output file, too. The q-value is set to the closest target score. |
add_decoy_proteins |
string | false |
true, false | If 'true' decoy proteins will be written to output file, too. The q-value is set to the closest target score. |
conservative |
string | true |
true, false | If 'true' (D+1)/T instead of (D+1)/(T+D) is used as a formula. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.