| OpenMS 2.5.0

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:

## 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...
virtual 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

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_ | ( |  | ) |

override protected virtual

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.