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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:
DefaultParamHandler

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...
 
IsobaricQuantifieroperator= (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...
 
virtual DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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_ ()
 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 IsobaricQuantitationMethodquant_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

- 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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
isotope_correction stringtrue true, falseEnable 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 stringfalse true, falseEnable 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:

Constructor & Destructor Documentation

IsobaricQuantifier ( const IsobaricQuantitationMethod *const  quant_method)
explicit

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

Parameters
quant_methodThe quantification method used for the data set to analyze.

Copy c'tor.

Member Function Documentation

void computeLabelingStatistics_ ( ConsensusMap consensus_map_out)
private

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

IsobaricQuantifier& operator= ( const IsobaricQuantifier rhs)

Assignment operator.

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_inRaw isobaric channel intensities from channel extraction.
consensus_map_outCorrected and normalized isobaric channel ratios for peptides.
Exceptions
Exception::FailedAPICallis least-squares fit fails
Exception::InvalidParameterif parameter is invalid (e.g. reference_channel)
void setDefaultParams_ ( )
protected

implemented for DefaultParamHandler

void updateMembers_ ( )
protectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

bool isotope_correction_enabled_
private

Is true if isotope correction is enabled, false otherwise.

bool normalization_enabled_
private

Is true if normalization is enabled, false otherwise.

const IsobaricQuantitationMethod* quant_method_
private

The quantification method used for the dataset to be analyzed.

Stats of current quantitation run.


OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:53 using doxygen 1.8.9.1