OpenMS  2.8.0
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
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:
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Collaboration diagram for IsobaricQuantifier:
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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_ () 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 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

- 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< 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.

Constructor & Destructor Documentation

◆ IsobaricQuantifier() [1/2]

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.

◆ IsobaricQuantifier() [2/2]

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_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)

◆ 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_

Stats of current quantitation run.