A simple calibration method using linear interpolation of given reference masses. More...

#include <OpenMS/FILTERING/CALIBRATION/InternalCalibration.h>

Inheritance diagram for InternalCalibration:

Public Member Functions
	InternalCalibration ()
	Default constructor.
	~InternalCalibration ()
	Destructor.
template<typename InputPeakType >
void	calibrateMapSpectrumwise (const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< DoubleReal > &ref_masses)
	Calibrate a peak map using given reference masses with a separate calibration function for each spectrum.
template<typename InputPeakType >
void	calibrateMapGlobally (const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< DoubleReal > &ref_masses, String trafo_file_name="")
	Calibrate a peak map using given reference masses with one calibration function for the whole map.
template<typename InputPeakType >
void	calibrateMapGlobally (const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< PeptideIdentification > &ref_ids, String trafo_file_name="")
	Calibrate a peak map using given reference ids with one calibration function for the whole map.
void	calibrateMapGlobally (const FeatureMap<> &feature_map, FeatureMap<> &calibrated_feature_map, String trafo_file_name="")
	Calibrate an annotated feature map with one calibration function for the whole map.
void	calibrateMapGlobally (const FeatureMap<> &feature_map, FeatureMap<> &calibrated_feature_map, std::vector< PeptideIdentification > &ref_ids, String trafo_file_name="")
	Calibrate a feature map using given reference ids with one calibration function for the whole map.
template<typename InputPeakType >
void	calibrateMapList (std::vector< MSExperiment< InputPeakType > > &exp_list, std::vector< MSExperiment< InputPeakType > > &calibrated_exp_list, std::vector< DoubleReal > &ref_masses, std::vector< DoubleReal > &detected_background_masses)
Protected Member Functions
void	makeLinearRegression_ (std::vector< DoubleReal > &observed_masses, std::vector< DoubleReal > &theoretical_masses)
	the actual calibration function
void	checkReferenceIds_ (std::vector< PeptideIdentification > &pep_ids)
	check if reference ids contain RT and MZ information as meta values
void	checkReferenceIds_ (const FeatureMap<> &feature_map)
	check if reference ids contain RT and MZ information as meta values
void	applyTransformation_ (const FeatureMap<> &feature_map, FeatureMap<> &calibrated_feature_map)
	apply transformation to all features (including subordinates and convex hulls)
Protected Attributes
TransformationDescription	trafo_
	here the transformation is stored

Detailed Description

A simple calibration method using linear interpolation of given reference masses.

This class implements a simle calibration method: given a list of reference masses, the relative errors of the peaks in the data are approximated by linear interpolation and subtracted from the data.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
mz_tolerance	float	1	min: 0	Allowed tolerance between peak and reference m/z.
mz_tolerance_unit	string	Da	Da, ppm	Unit for mz_tolerance.
rt_tolerance	int	10		Allowed tolerance between peak and reference rt.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

InternalCalibration ( )

Default constructor.

~InternalCalibration ( ) [inline]

Destructor.

Member Function Documentation

void applyTransformation_	(	const FeatureMap<> &	feature_map,
		FeatureMap<> &	calibrated_feature_map
	)			`[protected]`

apply transformation to all features (including subordinates and convex hulls)

void calibrateMapGlobally	(	const FeatureMap<> &	feature_map,
		FeatureMap<> &	calibrated_feature_map,
		std::vector< PeptideIdentification > &	ref_ids,
		String	trafo_file_name = `""`
	)

Calibrate a feature map using given reference ids with one calibration function for the whole map.

Calibrate a feature map using given peptide identifications. The calibration function is calculated for the whole map. Even if the features are already annotated with peptide ids these annotations are ignored for the calibration, only the reference ids are used. The m/z-values of the reference identifications are calculated through the given sequence and charge of the peptide. The reference ids are mapped onto the FeatureMap using IDMapper with the mz_tolerance and rt_tolerance parameters.

Parameters:

	feature_map	the uncalibrated feature map
	calibrated_feature_map	the calibrated feature map
	ref_ids	the reference peptide identifications
	trafo_file_name	file where the transformation function of the calibration is stored

void calibrateMapGlobally	(	const MSExperiment< InputPeakType > &	exp,
		MSExperiment< InputPeakType > &	calibrated_exp,
		std::vector< DoubleReal > &	ref_masses,
		String	trafo_file_name = `""`
	)

Calibrate a peak map using given reference masses with one calibration function for the whole map.

The calibration function is calculated for the whole map. For the matching of the reference masses and the peaks the parameter mz_tolerance is used to calculate a window around the reference masses. If more than one peak is found within this window the closest peak is taken.

Parameters:

	exp	the uncalibrated peak map
	calibrated_exp	the calibrated peak map
	ref_masses	the reference m/z values
	trafo_file_name	file where the transformation function of the calibration is stored

References TransformationDescription::apply(), ProgressLogger::endProgress(), Param::getValue(), InternalCalibration::makeLinearRegression_(), DefaultParamHandler::param_, ProgressLogger::setProgress(), ProgressLogger::startProgress(), and InternalCalibration::trafo_.

void calibrateMapGlobally	(	const FeatureMap<> &	feature_map,
		FeatureMap<> &	calibrated_feature_map,
		String	trafo_file_name = `""`
	)

Calibrate an annotated feature map with one calibration function for the whole map.

Calibrate an annotated (!) feature map using the features' identifications. The calibration function is calculated for the whole map. The m/z-values of the reference identifications are calculated through the given sequence and charge of the peptide.

Parameters:

	feature_map	the uncalibrated feature map (annotated with peptide ids)
	calibrated_feature_map	the calibrated feature map
	trafo_file_name	file where the transformation function of the calibration is stored

void calibrateMapGlobally	(	const MSExperiment< InputPeakType > &	exp,
		MSExperiment< InputPeakType > &	calibrated_exp,
		std::vector< PeptideIdentification > &	ref_ids,
		String	trafo_file_name = `""`
	)

Calibrate a peak map using given reference ids with one calibration function for the whole map.

Calibrate a map using given peptide identifications. The calibration function is calculated for the whole map. The m/z-values of the reference identifications are calculated through the given sequence and charge of the peptide. For the matching of the reference masses and the peaks the parameter mz_tolerance is used to calculate a window around the reference masses. If more than one peak is found within this window the closest peak is taken.

Parameters:

	exp	the uncalibrated peak map
	calibrated_exp	the calibrated peak map
	ref_ids	the reference peptide identifications
	trafo_file_name	file where the transformation function of the calibration is stored

References TransformationDescription::apply(), InternalCalibration::checkReferenceIds_(), Residue::Full, Param::getValue(), InternalCalibration::makeLinearRegression_(), DefaultParamHandler::param_, MSExperiment< PeakT, ChromatogramPeakT >::RTBegin(), and InternalCalibration::trafo_.

void calibrateMapList	(	std::vector< MSExperiment< InputPeakType > > &	exp_list,
		std::vector< MSExperiment< InputPeakType > > &	calibrated_exp_list,
		std::vector< DoubleReal > &	ref_masses,
		std::vector< DoubleReal > &	detected_background_masses
	)

void calibrateMapSpectrumwise	(	const MSExperiment< InputPeakType > &	exp,
		MSExperiment< InputPeakType > &	calibrated_exp,
		std::vector< DoubleReal > &	ref_masses
	)

Calibrate a peak map using given reference masses with a separate calibration function for each spectrum.

The calibration function is calculated for each spectrum separately. If not enough reference masses are found for a spectrum it is left uncalibrated. For the matching of the reference masses and the peaks, the parameter mz_tolerance is used to calculate a window around the reference masses. If more than one peak is found within this window the closest peak is taken.

Parameters: