OpenMS
NuXLFDR Class Reference

adapted FDR calculation for NA cross-links More...

#include <OpenMS/ANALYSIS/NUXL/NuXLFDR.h>

Collaboration diagram for NuXLFDR:
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Public Member Functions

 NuXLFDR (size_t report_top_hits)
 
void splitIntoPeptidesAndXLs (const PeptideIdentificationList &peptide_ids, PeptideIdentificationList &pep_pi, PeptideIdentificationList &xl_pi) const
 
void mergePeptidesAndXLs (const PeptideIdentificationList &pep_pi, const PeptideIdentificationList &xl_pi, PeptideIdentificationList &peptide_ids) const
 
void QValueAtPSMLevel (PeptideIdentificationList &peptide_ids) const
 
void calculatePeptideAndXLQValueAtPSMLevel (const PeptideIdentificationList &peptide_ids, PeptideIdentificationList &pep_pi, PeptideIdentificationList &xl_pi) const
 
void calculatePeptideAndXLQValueAndFilterAtPSMLevel (const std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids, PeptideIdentificationList &pep, double peptide_PSM_qvalue_threshold, double peptide_peptide_qvalue_threshold, PeptideIdentificationList &xl_pi, std::vector< double > xl_PSM_qvalue_thresholds, std::vector< double > xl_peptidelevel_qvalue_thresholds, const String &out_idxml, int decoy_factor) const
 

Private Attributes

size_t report_top_hits_
 

Detailed Description

adapted FDR calculation for NA cross-links

Constructor & Destructor Documentation

◆ NuXLFDR()

NuXLFDR ( size_t  report_top_hits)
explicit

Member Function Documentation

◆ calculatePeptideAndXLQValueAndFilterAtPSMLevel()

void calculatePeptideAndXLQValueAndFilterAtPSMLevel ( const std::vector< ProteinIdentification > &  protein_ids,
const PeptideIdentificationList peptide_ids,
PeptideIdentificationList pep,
double  peptide_PSM_qvalue_threshold,
double  peptide_peptide_qvalue_threshold,
PeptideIdentificationList xl_pi,
std::vector< double >  xl_PSM_qvalue_thresholds,
std::vector< double >  xl_peptidelevel_qvalue_thresholds,
const String out_idxml,
int  decoy_factor 
) const

◆ calculatePeptideAndXLQValueAtPSMLevel()

void calculatePeptideAndXLQValueAtPSMLevel ( const PeptideIdentificationList peptide_ids,
PeptideIdentificationList pep_pi,
PeptideIdentificationList xl_pi 
) const

◆ mergePeptidesAndXLs()

void mergePeptidesAndXLs ( const PeptideIdentificationList pep_pi,
const PeptideIdentificationList xl_pi,
PeptideIdentificationList peptide_ids 
) const

◆ QValueAtPSMLevel()

void QValueAtPSMLevel ( PeptideIdentificationList peptide_ids) const

◆ splitIntoPeptidesAndXLs()

void splitIntoPeptidesAndXLs ( const PeptideIdentificationList peptide_ids,
PeptideIdentificationList pep_pi,
PeptideIdentificationList xl_pi 
) const

Member Data Documentation

◆ report_top_hits_

size_t report_top_hits_
private