PercolatorFeatureSetHelper

class pyopenms.PercolatorFeatureSetHelper

Bases: object

Cython implementation of _PercolatorFeatureSetHelper

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PercolatorFeatureSetHelper.html

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

__init__()

  • Cython signature: void PercolatorFeatureSetHelper()

  • Cython signature: void PercolatorFeatureSetHelper(PercolatorFeatureSetHelper &)

Methods

__init__

  • Cython signature: void PercolatorFeatureSetHelper()

addCOMETFeatures

Cython signature: void addCOMETFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

addCONCATSEFeatures

Cython signature: void addCONCATSEFeatures(libcpp_vector[PeptideIdentification] & peptide_id_list, StringList & search_engines_used, StringList & feature_set)

addMASCOTFeatures

Cython signature: void addMASCOTFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

addMSGFFeatures

Cython signature: void addMSGFFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

addMULTISEFeatures

Cython signature: void addMULTISEFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & search_engines_used, StringList & feature_set, bool complete_only, bool limits_imputation)

addXTANDEMFeatures

Cython signature: void addXTANDEMFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

checkExtraFeatures

Cython signature: void checkExtraFeatures(libcpp_vector[PeptideHit] & psms, StringList & extra_features)

concatMULTISEPeptideIds

Cython signature: void concatMULTISEPeptideIds(libcpp_vector[PeptideIdentification] & all_peptide_ids, libcpp_vector[PeptideIdentification] & new_peptide_ids, String search_engine)

mergeMULTISEPeptideIds

Cython signature: void mergeMULTISEPeptideIds(libcpp_vector[PeptideIdentification] & all_peptide_ids, libcpp_vector[PeptideIdentification] & new_peptide_ids, String search_engine)

mergeMULTISEProteinIds

Cython signature: void mergeMULTISEProteinIds(libcpp_vector[ProteinIdentification] & all_protein_ids, libcpp_vector[ProteinIdentification] & new_protein_ids)
addCOMETFeatures()

Cython signature: void addCOMETFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

addCONCATSEFeatures()

Cython signature: void addCONCATSEFeatures(libcpp_vector[PeptideIdentification] & peptide_id_list, StringList & search_engines_used, StringList & feature_set)

This struct can be used to store both peak or feature indices :param peptide_ids: PeptideIdentification vector to create Percolator features in :param search_engines_used: The list of search engines to be considered :param feature_set: Register of added features

addMASCOTFeatures()

Cython signature: void addMASCOTFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

addMSGFFeatures()

Cython signature: void addMSGFFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

addMULTISEFeatures()

Cython signature: void addMULTISEFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & search_engines_used, StringList & feature_set, bool complete_only, bool limits_imputation)

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

:param limits_imputation

addXTANDEMFeatures()

Cython signature: void addXTANDEMFeatures(libcpp_vector[PeptideIdentification] & peptide_ids, StringList & feature_set)

Parameters

  • peptide_ids – PeptideIdentification vector to create Percolator features in

  • feature_set – Register of added features

checkExtraFeatures()

Cython signature: void checkExtraFeatures(libcpp_vector[PeptideHit] & psms, StringList & extra_features)

Parameters

  • psms – The vector of PeptideHit to be checked

  • extra_features – The list of requested extra features

concatMULTISEPeptideIds()

Cython signature: void concatMULTISEPeptideIds(libcpp_vector[PeptideIdentification] & all_peptide_ids, libcpp_vector[PeptideIdentification] & new_peptide_ids, String search_engine)

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

mergeMULTISEPeptideIds()

Cython signature: void mergeMULTISEPeptideIds(libcpp_vector[PeptideIdentification] & all_peptide_ids, libcpp_vector[PeptideIdentification] & new_peptide_ids, String search_engine)

Parameters

  • all_peptide_idsL – PeptideIdentification vector to be merged into

  • new_peptide_idsL – PeptideIdentification vector to merge

  • search_engineL – Search engine to create features from their scores

mergeMULTISEProteinIds()

Cython signature: void mergeMULTISEProteinIds(libcpp_vector[ProteinIdentification] & all_protein_ids, libcpp_vector[ProteinIdentification] & new_protein_ids)

Parameters

  • all_protein_ids – ProteinIdentification vector to be merged into

  • new_protein_ids – ProteinIdentification vector to merge