OpenMS
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Percolator feature set and integration helper. More...
#include <OpenMS/ANALYSIS/ID/PercolatorFeatureSetHelper.h>
Classes | |
struct | lq_PeptideEvidence |
For accession dependent sorting of PeptideEvidences. More... | |
struct | lq_ProteinHit |
For accession dependent sorting of ProteinHits. More... | |
Static Public Member Functions | |
static void | concatMULTISEPeptideIds (std::vector< PeptideIdentification > &all_peptide_ids, std::vector< PeptideIdentification > &new_peptide_ids, const String &search_engine) |
concatMULTISEPeptideIds More... | |
static void | mergeMULTISEPeptideIds (std::vector< PeptideIdentification > &all_peptide_ids, std::vector< PeptideIdentification > &new_peptide_ids, const String &search_engine) |
mergeMULTISEPeptideIds More... | |
static void | mergeMULTISEProteinIds (std::vector< ProteinIdentification > &all_protein_ids, std::vector< ProteinIdentification > &new_protein_ids) |
mergeMULTISEProteinIds More... | |
static void | addMSGFFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set) |
addMSGFFeatures More... | |
static void | addXTANDEMFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set) |
addXTANDEMFeatures More... | |
static void | addCOMETFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set) |
addCOMETFeatures More... | |
static void | addMASCOTFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &feature_set) |
addMASCOTFeatures More... | |
static void | addMULTISEFeatures (std::vector< PeptideIdentification > &peptide_ids, StringList &search_engines_used, StringList &feature_set, bool complete_only=true, bool limits_imputation=false) |
addMULTISEFeatures More... | |
static void | addCONCATSEFeatures (std::vector< PeptideIdentification > &peptide_id_list, StringList &search_engines_used, StringList &feature_set) |
addCONCATSEFeatures More... | |
static void | checkExtraFeatures (const std::vector< PeptideHit > &psms, StringList &extra_features) |
checkExtraFeatures More... | |
static void | addMSFRAGGERFeatures (StringList &extra_features) |
addMSFraggerFeatures More... | |
Static Protected Member Functions | |
static double | rescaleFragmentFeature_ (double featureValue, int NumMatchedMainIons) |
Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator. More... | |
static void | assignDeltaScore_ (std::vector< PeptideHit > &hits, const String &score_ref, const String &output_ref) |
helper function for assigning the frequently occurring feature delta score More... | |
static String | getScanMergeKey_ (std::vector< PeptideIdentification >::iterator it, std::vector< PeptideIdentification >::iterator start) |
gets the scan identifier to merge by More... | |
Percolator feature set and integration helper.
This class contains functions to handle (compute, aggregate, integrate) Percolator features. This includes the calculation or extraction of Percolator features depending on the search engine(s) for later use with PercolatorAdapter. It also includes handling the reintegration of the percolator result into the set of Identifications.
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addCOMETFeatures
peptide_ids | PeptideIdentification vector to create Percolator features in |
feature_set | register of added features |
Creates and adds Comet specific Percolator features and registers them in feature_set
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addCONCATSEFeatures
peptide_id_list | PeptideIdentification vector to create Percolator features in |
search_engines_used | the list of search engines to be considered |
feature_set | register of added features |
Adds multiple search engine specific Percolator features and registers them in feature_set
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addMASCOTFeatures
peptide_ids | PeptideIdentification vector to create Percolator features in |
feature_set | register of added features |
Creates and adds Mascot specific Percolator features and registers them in feature_set
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static |
addMSFraggerFeatures
extra_features | register of added features |
Registers the MSFragger specific Percolator features in extra_features.
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addMSGFFeatures
peptide_ids | PeptideIdentification vector to create Percolator features in |
feature_set | register of added features |
Creates and adds MSGF+ specific Percolator features and registers them in feature_set. MSGF+ should be run with the addFeatures flag enabled.
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addMULTISEFeatures
peptide_ids | PeptideIdentification vector to create Percolator features in |
search_engines_used | the list of search engines to be considered |
feature_set | register of added features |
complete_only | will only add features for PeptideIdentifications where all given search engines identified something |
limits_imputation | Adds multiple search engine specific Percolator features and registers them in feature_set |
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addXTANDEMFeatures
peptide_ids | PeptideIdentification vector to create Percolator features in |
feature_set | register of added features |
Creates and adds X!Tandem specific Percolator features and registers them in feature_set
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staticprotected |
helper function for assigning the frequently occurring feature delta score
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checkExtraFeatures
psms | the vector of PeptideHit to be checked |
extra_features | the list of requested extra features |
checks and removes requested extra Percolator features that are actually unavailable (to compute)
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concatMULTISEPeptideIds
all_peptide_ids | PeptideIdentification vector to append to |
new_peptide_ids | PeptideIdentification vector to be appended |
search_engine | search engine to depend on for feature creation |
Appends a vector of PeptideIdentification to another and prepares Percolator features in MetaInfo (With the respective key "CONCAT:" + search_engine).
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staticprotected |
gets the scan identifier to merge by
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static |
mergeMULTISEPeptideIds
all_peptide_ids | PeptideIdentification vector to be merged into |
new_peptide_ids | PeptideIdentification vector to merge |
search_engine | search engine to create features from their scores |
Merges a vector of PeptideIdentification into another and prepares the merged MetaInfo and scores for collection in addMULTISEFeatures for feature registration.
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mergeMULTISEProteinIds
all_protein_ids | ProteinIdentification vector to be merged into |
new_protein_ids | ProteinIdentification vector to merge |
Concatenates SearchParameter of multiple search engine runs and merges PeptideEvidences, collects used search engines in MetaInfo for collection in addMULTISEFeatures for feature registration.
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staticprotected |
Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator.