This class is a metric for the QualityControl-ToppTool. More...

#include <OpenMS/QC/Ms2IdentificationRate.h>

Inheritance diagram for Ms2IdentificationRate:

Classes
struct	IdentificationRateData
	Structure for storing results. More...

Public Member Functions
	Ms2IdentificationRate ()=default
	Default constructor. More...

virtual	~Ms2IdentificationRate ()=default
	Destructor. More...

void	compute (const FeatureMap &feature_map, const MSExperiment &exp, bool force_fdr=false)
	computes Ms2 Identification Rate More...

const String &	getName () const override
	returns the name of the metric More...

const std::vector< IdentificationRateData > &	getResults () const
	returns results More...

QCBase::Status	requires () const override
	Returns the input data requirements of the compute(...) function. More...

Private Attributes
const String	name_ = "Ms2IdentificationRate"
	name of the metric More...

std::vector< IdentificationRateData >	rate_result_
	container that stores results More...

Additional Inherited Members
Public Types inherited from QCBase
enum	Requires : UInt64 { FAIL, RAWMZML, POSTFDRFEAT, PREFDRFEAT, CONTAMINANTS, TRAFOALIGN, SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...

Static Public Member Functions inherited from QCBase
template<typename MAP , typename T >
static void	iterateFeatureMap (MAP &fmap, T lambda)
	function, which iterates through all PeptideIdentifications of a given FeatureMap and applies a given lambda function More...

Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires More...

Detailed Description

This class is a metric for the QualityControl-ToppTool.

This class computes the MS2 Identification Rate (as #identified PSMs divided by total number of MS2 scans) given a FeatureMap and an MSExperiment. Only pep-ids with FDR metavalue 'target_decoy' equal to 'target' are counted, unless force_fdr flag is set (assumes all pep-ids are target peptides)

Class Documentation

◆ OpenMS::Ms2IdentificationRate::IdentificationRateData

struct OpenMS::Ms2IdentificationRate::IdentificationRateData

Structure for storing results.

Class Members
double	identification_rate
UInt64	num_ms2_spectra
UInt64	num_peptide_identification

Constructor & Destructor Documentation

◆ Ms2IdentificationRate()

Ms2IdentificationRate ( )

default

Default constructor.

◆ ~Ms2IdentificationRate()

virtual ~Ms2IdentificationRate ( )

virtualdefault

Destructor.

Member Function Documentation

◆ compute()

void compute	(	const FeatureMap &	feature_map,
		const MSExperiment &	exp,
		bool	force_fdr = `false`
	)

computes Ms2 Identification Rate

stores results as a struct in a vector Only pep-ids with FDR metavalue annotation as 'target' are counted, unless force_fdr flag is set (assumes all pep-ids are target peptides)

Parameters

feature_map	Input FeatureMap with target/decoy annotation
exp	MSExperiment for counting number of MS2 spectra
force_fdr	Count all(!) PepIDs towards number of identified MS2 spectra (ignore target/decoy information if any)

Exceptions

Exception::MissingInformation	is thrown if the FeatureXML is empty
Exception::MissingInformation	is thrown if the mzML is empty
Exception::MissingInformation	is thrown if the experiment doesn't contain MS2 spectra
Exception::Precondition	is thrown if there are more identifications than MS2 spectra

◆ getName()

const String& getName ( ) const

overridevirtual

returns the name of the metric

Implements QCBase.

◆ getResults()

const std::vector<IdentificationRateData>& getResults ( ) const

returns results

◆ requires()

QCBase::Status requires ( ) const

overridevirtual

Returns the input data requirements of the compute(...) function.

Returns: Status for RAWMZML and POSTFDRFEAT

Implements QCBase.

Member Data Documentation

◆ name_

const String name_ = "Ms2IdentificationRate"

private

name of the metric

◆ rate_result_

std::vector<IdentificationRateData> rate_result_