TIC Class Reference

Total Ion Current (TIC) as a QC metric. More...

#include <OpenMS/QC/TIC.h>

Inheritance diagram for TIC:

Collaboration diagram for TIC:

Classes
struct	Result
	Computed Total Ion Current trace plus stability counters. More...

Public Member Functions
	TIC ()=default
	Default constructor.
virtual	~TIC ()=default
	Destructor.
Result	compute (const MSExperiment &exp, float bin_size=0, UInt ms_level=1)
	Compute the Total Ion Current trace and stability metrics.
const std::string &	getName () const override
	Name of this QC metric ("TIC").
const std::vector< MSChromatogram > &	getResults () const
QCBase::Status	requirements () const override
	Input-data requirements of compute (raw mzML data).
void	addMetaDataMetricsToMzTab (MzTabMetaData &meta, const std::vector< Result > &tics)
	Append the TIC traces from tics to the MTD section of meta as custom parameters.
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Private Attributes
const std::string	name_ = "TIC"

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
template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ?
Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires
static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit

Detailed Description

Total Ion Current (TIC) as a QC metric.

Builds a Total Ion Current trace at a chosen MS level from an MSExperiment and returns a Result that bundles the per-bin intensities, the relative intensities (0 – 100), the retention times, the area under the TIC and two stability counters that flag abrupt 10-fold intensity changes between consecutive bins. Each call to compute is independent; results are returned to the caller and not retained by the instance.

Constructor & Destructor Documentation

TIC()

TIC ( )

default

Default constructor.

~TIC()

virtual ~TIC ( )

virtualdefault

Destructor.

Member Function Documentation

addMetaDataMetricsToMzTab()

void addMetaDataMetricsToMzTab	(	MzTabMetaData &	meta,
		const std::vector< Result > &	tics
	)

Append the TIC traces from tics to the MTD section of meta as custom parameters.

For every non-empty entry in tics one custom parameter is added to meta, named TIC_1, TIC_2, ... (1-based index into tics), with the controlled-vocabulary label "total ion current" (MS:1000285). The value is a flat list of [rt0,int0,rt1,int1,...] pairs taken from Result::retention_times and Result::intensities.

Parameters

[in,out]	meta	mzTab metadata section to extend.
[in]	tics	TIC results to serialise; empty entries are skipped.

compute()

Result compute	(	const MSExperiment &	exp,
		float	bin_size = 0,
		UInt	ms_level = 1
	)

Compute the Total Ion Current trace and stability metrics.

Builds the TIC at the requested MS level. When bin_size is positive, intensities are summed within bin_size second retention-time bins; when bin_size is 0, no resampling is applied and the trace contains one entry per source spectrum.

The returned Result is empty when exp has no spectra of MS level ms_level.

Parameters

[in]	exp	Source experiment.
[in]	bin_size	RT bin size in seconds; 0 disables binning.
[in]	ms_level	MS level whose spectra are aggregated.

Returns

Computed metrics. The Result::intensities and Result::retention_times are empty when no spectra of ms_level are present.

getName()

const std::string & getName ( ) const

overridevirtual

Name of this QC metric ("TIC").

Implements QCBase.

getResults()

const std::vector< MSChromatogram > & getResults

(

)

const

requirements()

QCBase::Status requirements ( ) const

overridevirtual

Input-data requirements of compute (raw mzML data).

Implements QCBase.

Member Data Documentation

name_

const std::string name_ = "TIC"

private