Ms2IdentificationRate Class Reference

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

#include <OpenMS/QC/Ms2IdentificationRate.h>

Inheritance diagram for Ms2IdentificationRate:

Collaboration 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 assume_all_target=false)
	computes Ms2 Identification Rate with FeatureMap More...
void	compute (const std::vector< PeptideIdentification > &pep_ids, const MSExperiment &exp, bool assume_all_target=false)
	computes Ms2 Identification Rate with PeptideIdentifications More...
const String &	getName () const override
	returns the name of the metric More...
const std::vector< IdentificationRateData > &	getResults () const
	returns results More...
QCBase::Status	requirements () const override
	Returns the input data requirements of the compute(...) function. More...
void	addMetaDataMetricsToMzTab (MzTabMetaData &meta) const
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Private Member Functions
Size	getMS2Count_ (const MSExperiment &exp)
	returns number of all ms2 spectra in an MSExperiment More...
void	writeResults_ (Size pep_ids_count, Size ms2_spectra_count)

Static Private Member Functions
static bool	isTargetPeptide_ (const PeptideIdentification &id, bool all_targets)

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 class	Requires : UInt64 {   NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT ,   CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...
enum class	ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT }
using	Status = FlagSet< Requires >
Static Public Member Functions inherited from QCBase
static bool	isLabeledExperiment (const ConsensusMap &cm)
	check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More...
template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ? More...
Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires More...
static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit 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 assume_all_target flag is set (assumes all pep-ids are target peptides)

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Class Documentation

OpenMS::Ms2IdentificationRate::IdentificationRateData

struct OpenMS::Ms2IdentificationRate::IdentificationRateData

Structure for storing results.

Collaboration diagram for Ms2IdentificationRate::IdentificationRateData:

Class Members
double	identification_rate
Size	num_ms2_spectra
Size	num_peptide_identification

Constructor & Destructor Documentation

Ms2IdentificationRate()

Ms2IdentificationRate ( )

default

Default constructor.

~Ms2IdentificationRate()

virtual ~Ms2IdentificationRate ( )

virtualdefault

Destructor.

Member Function Documentation

addMetaDataMetricsToMzTab()

void addMetaDataMetricsToMzTab

(

MzTabMetaData &

meta

)

const

compute() [1/2]

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

computes Ms2 Identification Rate with FeatureMap

stores results as a struct in a vector Only pep-ids with target/decoy annotation as 'target' are counted, unless force_index 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
assume_all_target	Count all(!) PepIDs towards number of identified MS2 spectra (ignore target/decoy information if any)

Exceptions

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

compute() [2/2]

void compute	(	const std::vector< PeptideIdentification > &	pep_ids,
		const MSExperiment &	exp,
		bool	assume_all_target = false
	)

computes Ms2 Identification Rate with PeptideIdentifications

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

Parameters

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

Exceptions

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

getMS2Count_()

Size getMS2Count_ ( const MSExperiment &  exp )

private

returns number of all ms2 spectra in an MSExperiment

getName()

const String& getName ( ) const

overridevirtual

returns the name of the metric

Implements QCBase.

getResults()

const std::vector<IdentificationRateData>& getResults

(

)

const

returns results

isTargetPeptide_()

static bool isTargetPeptide_ ( const PeptideIdentification &  id, bool  all_targets  )

staticprivate

requirements()

QCBase::Status requirements ( ) const

overridevirtual

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

Returns

Status for RAWMZML and POSTFDRFEAT

Implements QCBase.

writeResults_()

void writeResults_ ( Size  pep_ids_count, Size  ms2_spectra_count  )

private

Member Data Documentation

name_

const String name_ = "Ms2IdentificationRate"

private

name of the metric

rate_result_

std::vector<IdentificationRateData> rate_result_

private

container that stores results