NuXLFDR Class Reference

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

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

Collaboration diagram for NuXLFDR:

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