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, String search_engine)
	concatMULTISEPeptideIds More...

static void	mergeMULTISEPeptideIds (std::vector< PeptideIdentification > &all_peptide_ids, std::vector< PeptideIdentification > &new_peptide_ids, 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, String score_ref, 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...

Detailed Description

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.

Member Function Documentation

◆ addCOMETFeatures()

static void addCOMETFeatures	(	std::vector< PeptideIdentification > &	peptide_ids,
		StringList &	feature_set
	)

static

addCOMETFeatures

Parameters

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

◆ addCONCATSEFeatures()

static void addCONCATSEFeatures	(	std::vector< PeptideIdentification > &	peptide_id_list,
		StringList &	search_engines_used,
		StringList &	feature_set
	)

static

addCONCATSEFeatures

Parameters

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

◆ addMASCOTFeatures()

static void addMASCOTFeatures	(	std::vector< PeptideIdentification > &	peptide_ids,
		StringList &	feature_set
	)

static

addMASCOTFeatures

Parameters

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

◆ addMSFRAGGERFeatures()

static void addMSFRAGGERFeatures ( StringList & extra_features )

static

addMSFraggerFeatures

Parameters

extra_features register of added features

Registers the MSFragger specific Percolator features in extra_features.

◆ addMSGFFeatures()

static void addMSGFFeatures	(	std::vector< PeptideIdentification > &	peptide_ids,
		StringList &	feature_set
	)

static

addMSGFFeatures

Parameters

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.

◆ addMULTISEFeatures()

static void addMULTISEFeatures	(	std::vector< PeptideIdentification > &	peptide_ids,
		StringList &	search_engines_used,
		StringList &	feature_set,
		bool	complete_only = `true`,
		bool	limits_imputation = `false`
	)

static

addMULTISEFeatures

Parameters

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

◆ addXTANDEMFeatures()

static void addXTANDEMFeatures	(	std::vector< PeptideIdentification > &	peptide_ids,
		StringList &	feature_set
	)

static

addXTANDEMFeatures

Parameters

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

◆ assignDeltaScore_()

static void assignDeltaScore_	(	std::vector< PeptideHit > &	hits,
		String	score_ref,
		String	output_ref
	)

staticprotected

helper function for assigning the frequently occurring feature delta score

◆ checkExtraFeatures()

static void checkExtraFeatures	(	const std::vector< PeptideHit > &	psms,
		StringList &	extra_features
	)

static

checkExtraFeatures

Parameters

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)

◆ concatMULTISEPeptideIds()

static void concatMULTISEPeptideIds	(	std::vector< PeptideIdentification > &	all_peptide_ids,
		std::vector< PeptideIdentification > &	new_peptide_ids,
		String	search_engine
	)

static

concatMULTISEPeptideIds

Parameters

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).

◆ getScanMergeKey_()

static String getScanMergeKey_	(	std::vector< PeptideIdentification >::iterator	it,
		std::vector< PeptideIdentification >::iterator	start
	)

staticprotected

gets the scan identifier to merge by

◆ mergeMULTISEPeptideIds()

static void mergeMULTISEPeptideIds	(	std::vector< PeptideIdentification > &	all_peptide_ids,
		std::vector< PeptideIdentification > &	new_peptide_ids,
		String	search_engine
	)

static

mergeMULTISEPeptideIds

Parameters

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.

◆ mergeMULTISEProteinIds()

static void mergeMULTISEProteinIds	(	std::vector< ProteinIdentification > &	all_protein_ids,
		std::vector< ProteinIdentification > &	new_protein_ids
	)

static

mergeMULTISEProteinIds

Parameters

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.

◆ rescaleFragmentFeature_()

static double rescaleFragmentFeature_	(	double	featureValue,
		int	NumMatchedMainIons
	)

staticprotected

Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator.

Classes

Static Public Member Functions

Static Protected Member Functions

Detailed Description

Member Function Documentation

◆ addCOMETFeatures()

◆ addCONCATSEFeatures()

◆ addMASCOTFeatures()

◆ addMSFRAGGERFeatures()

◆ addMSGFFeatures()

◆ addMULTISEFeatures()

◆ addXTANDEMFeatures()

◆ assignDeltaScore_()

◆ checkExtraFeatures()

◆ concatMULTISEPeptideIds()

◆ getScanMergeKey_()

◆ mergeMULTISEPeptideIds()

◆ mergeMULTISEProteinIds()

◆ rescaleFragmentFeature_()