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.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
isotope_correction	string	true	true, false	Enable isotope correction (highly recommended). Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results.
normalization	string	false	true, false	Enable normalization of channel intensities with respect to the reference channel. The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!

Note:

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

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.