Given the extracted channel intensities the IsobaricQuantifier corrects and normalizes the intensities for further processing. More...
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifier.h>
 
  
 | 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 ¶m) | 
| 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_ () | 
| 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... | |
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! | 
| IsobaricQuantifier | ( | const IsobaricQuantitationMethod *const | quant_method | ) | 
Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex).
| quant_method | The quantification method used for the data set to analyze. | 
| IsobaricQuantifier | ( | const IsobaricQuantifier & | other | ) | 
Copy c'tor.
| 
 | 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).
| consensus_map_in | Raw isobaric channel intensities from channel extraction. | 
| consensus_map_out | Corrected and normalized isobaric channel ratios for peptides. | 
| Exception::FailedAPICall | is least-squares fit fails | 
| Exception::InvalidParameter | if parameter is invalid (e.g. reference_channel) | 
| 
 | protected | 
implemented for DefaultParamHandler
| 
 | protectedvirtual | 
implemented for DefaultParamHandler
Reimplemented from DefaultParamHandler.
| 
 | private | 
Is true if isotope correction is enabled, false otherwise.
| 
 | private | 
Is true if normalization is enabled, false otherwise.
| 
 | private | 
The quantification method used for the dataset to be analyzed.
| 
 | private | 
Stats of current quantitation run.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |