OpenMS
2.5.0
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A class containing correction functions for Swath MS maps. More...
#include <OpenMS/ANALYSIS/OPENSWATH/SwathMapMassCorrection.h>
Public Member Functions | |
SwathMapMassCorrection () | |
Constructor. More... | |
~SwathMapMassCorrection ()=default | |
Destructor. More... | |
void | updateMembers_ () override |
Synchronize members with param class. More... | |
void | correctMZ (const std::map< String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > &transition_group_map, std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &targeted_exp) |
Correct the m/z values of a SWATH map based on the RT-normalization peptides. More... | |
void | correctIM (const std::map< String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > &transition_group_map, const std::vector< OpenSwath::SwathMap > &swath_maps, TransformationDescription &im_trafo, const OpenSwath::LightTargetedExperiment &targeted_exp) |
Correct the ion mobility values of a SWATH map based on the RT-normalization peptides. 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... | |
Additional Inherited Members | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. 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... | |
A class containing correction functions for Swath MS maps.
This class can use a set of pre-determined points in a Swath-MS map to correct all maps according to the m/z shift found in those fixed points.
Constructor.
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default |
Destructor.
void correctIM | ( | const std::map< String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > & | transition_group_map, |
const std::vector< OpenSwath::SwathMap > & | swath_maps, | ||
TransformationDescription & | im_trafo, | ||
const OpenSwath::LightTargetedExperiment & | targeted_exp | ||
) |
Correct the ion mobility values of a SWATH map based on the RT-normalization peptides.
This extracts the full spectra at the most likely elution time of the calibrant peptides and fits a linear regression curve to correct for a possible ion mobility (drift time) shift of the empirical drift time vs the theoretically expected drift time.
transition_group_map | A MRMFeatureFinderScoring result map |
swath_maps | The raw swath maps from the current run |
im_trafo | The resulting map containing the transformation |
void correctMZ | ( | const std::map< String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > & | transition_group_map, |
std::vector< OpenSwath::SwathMap > & | swath_maps, | ||
const OpenSwath::LightTargetedExperiment & | targeted_exp | ||
) |
Correct the m/z values of a SWATH map based on the RT-normalization peptides.
This extracts the full spectra at the most likely elution time of the calibrant peptides and fits a regression curve to correct for a possible mass shift of the empirical masses vs the theoretically expected masses. Several types of regressions are available (see below corr_type parameter).
The function will replace the pointers stored in swath_maps with a transforming map that will contain corrected m/z values.
transition_group_map | A MRMFeatureFinderScoring result map |
swath_maps | The raw swath maps from the current run |
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overridevirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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