OpenMS
2.8.0
|
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_ () 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 | |
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< 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.
|
explicit |
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
|
overrideprotectedvirtual |
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.