IsobaricQuantifier Class Reference

Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing. More...

#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifier.h>

Inheritance diagram for IsobaricQuantifier:

Collaboration diagram for IsobaricQuantifier:

Public Member Functions
	IsobaricQuantifier (const IsobaricQuantitationMethod *const quant_method)
	Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex). More...
	IsobaricQuantifier (const IsobaricQuantifier &other)
	Copy c'tor. More...
IsobaricQuantifier &	operator= (const IsobaricQuantifier &rhs)
	Assignment operator. More...
void	quantify (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out)
	Using the raw isobaric intensities we apply isotope correction, normalization (using median). More...
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...
virtual	~DefaultParamHandler ()
	Destructor. More...
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...
void	setParameters (const Param &param)
	Sets the parameters. More...
const Param &	getParameters () const
	Non-mutable access to the parameters. More...
const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...
const String &	getName () const
	Non-mutable access to the name. More...
void	setName (const String &name)
	Mutable access to the name. More...
const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
void	setDefaultParams_ ()
	implemented for DefaultParamHandler More...
void	updateMembers_ () override
	implemented for DefaultParamHandler More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Member Functions
void	computeLabelingStatistics_ (ConsensusMap &consensus_map_out)
	Computes labeling statistics (efficiency, number of empty scans,...) More...

Private Attributes
IsobaricQuantifierStatistics	stats_
	Stats of current quantitation run. More...
const IsobaricQuantitationMethod *	quant_method_
	The quantification method used for the dataset to be analyzed. More...
bool	isotope_correction_enabled_
	Is true if isotope correction is enabled, false otherwise. More...
bool	normalization_enabled_
	Is true if normalization is enabled, false otherwise. More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String	error_name_
	Name that is displayed in error messages during the parameter checking. More...
bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing.

Constructor & Destructor Documentation

IsobaricQuantifier() [1/2]

IsobaricQuantifier ( const IsobaricQuantitationMethod *const  quant_method )

explicit

Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex).

Parameters

quant_method

The quantification method used for the data set to analyze.

IsobaricQuantifier() [2/2]

IsobaricQuantifier

(

const IsobaricQuantifier &

other

)

Copy c'tor.

Member Function Documentation

computeLabelingStatistics_()

void computeLabelingStatistics_ ( ConsensusMap &  consensus_map_out )

private

Computes labeling statistics (efficiency, number of empty scans,...)

operator=()

IsobaricQuantifier& operator=

(

const IsobaricQuantifier &

rhs

)

Assignment operator.

quantify()

void quantify	(	const ConsensusMap &	consensus_map_in,
		ConsensusMap &	consensus_map_out
	)

Using the raw isobaric intensities we apply isotope correction, normalization (using median).

Parameters

consensus_map_in	Raw isobaric channel intensities from channel extraction.
consensus_map_out	Corrected and normalized isobaric channel ratios for peptides.

Exceptions

Exception::FailedAPICall	is least-squares fit fails
Exception::InvalidParameter	if parameter is invalid (e.g. reference_channel)

setDefaultParams_()

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

isotope_correction_enabled_

bool isotope_correction_enabled_

private

Is true if isotope correction is enabled, false otherwise.

normalization_enabled_

bool normalization_enabled_

private

Is true if normalization is enabled, false otherwise.

quant_method_

const IsobaricQuantitationMethod* quant_method_

private

The quantification method used for the dataset to be analyzed.

stats_

IsobaricQuantifierStatistics stats_

private

Stats of current quantitation run.