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) |
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protected |
implemented for DefaultParamHandler
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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 |