| OpenMS 2.5.0

Classes | Static Public Member Functions | Static Protected Member Functions | List of all members
PercolatorFeatureSetHelper Class Reference

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 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

## ◆ 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
| ) |  |

static protected

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
| ) |  |

static protected

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
| ) |  |

static protected

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