The MRMFeatureFinder finds and scores peaks of transitions that co-elute. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
Public Types | |
typedef MSSpectrum< ChromatogramPeak > | RichPeakChromatogram |
Type definitions. More... | |
typedef OpenSwath::LightTransition | TransitionType |
typedef OpenSwath::LightTargetedExperiment | TargetedExpType |
typedef OpenSwath::LightPeptide | PeptideType |
typedef OpenSwath::LightProtein | ProteinType |
typedef OpenSwath::LightModification | ModificationType |
typedef MRMTransitionGroup< MSSpectrum< ChromatogramPeak >, TransitionType > | MRMTransitionGroupType |
typedef std::map< String, MRMTransitionGroupType > | TransitionGroupMapType |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Public Member Functions | |
MRMFeatureFinderScoring () | |
Constructor. More... | |
~MRMFeatureFinderScoring () | |
Destructor. More... | |
void | scorePeakgroups (MRMTransitionGroupType &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap &output) |
Score all peak groups of a transition group. More... | |
void | setStrictFlag (bool f) |
Set the flag for strict mapping. More... | |
void | setMS1Map (OpenSwath::SpectrumAccessPtr ms1_map) |
Add an MS1 map containing spectra. More... | |
void | mapExperimentToTransitionList (OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window) |
Map the chromatograms to the transitions. More... | |
void | pickExperiment (MSExperiment< Peak1D > &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, MSExperiment< Peak1D > &swath_map) |
Picker and prepare functions. More... | |
void | pickExperiment (OpenSwath::SpectrumAccessPtr input, FeatureMap &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map) |
Pick features in one experiment containing chromatogram. More... | |
void | prepareProteinPeptideMaps_ (OpenSwath::LightTargetedExperiment &transition_exp) |
Prepares the internal mappings of peptides and proteins. More... | |
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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... | |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
Private Member Functions | |
void | updateMembers_ () |
Synchronize members with param class. More... | |
Additional Inherited Members | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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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... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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static int | recursion_depth_ |
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
It does so using an internal peakpicker for each chromatogram and then creating consensus / meta-peaks (MRMFeatures) that contain the information of all corresponding chromatograms at the peak-position. It then goes on to score those MRMFeatures using different criteria described in the MRMScoring class.
Internally, all peak group detection is performed in MRMTransitionGroupPicker which segments the data and determines consensus peaks across traces (MRMFeatures). All scoring is delegated to the OpenSwathScoring class which implements i) chromatographic scores, ii) library based scores and iii) full spectrum (DIA) scores. These scores are retrieved from the OpenSwathScoring class and added to the MRMFeatures found in this algorithm. Note that the OpenSwathScoring is a facade that can be used to communicate with the underlying actual scoring engines and assembles the scores inside a scoring object called OpenSwath_Scores where they are easy to retrieve.
typedef OpenSwath::LightPeptide PeptideType |
typedef OpenSwath::LightProtein ProteinType |
Type definitions.
typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType |
Constructor.
Destructor.
void mapExperimentToTransitionList | ( | OpenSwath::SpectrumAccessPtr | input, |
OpenSwath::LightTargetedExperiment & | transition_exp, | ||
TransitionGroupMapType & | transition_group_map, | ||
TransformationDescription | trafo, | ||
double | rt_extraction_window | ||
) |
Map the chromatograms to the transitions.
Map an input chromatogram experiment (mzML) and transition list (TraML) onto each other when they share identifiers, e.g. if the transition id is the same as the chromatogram native id.
input | The input chromatograms |
transition_exp | The transition list describing the experiment |
transition_group_map | Mapping of transition groups |
trafo | Optional transformation of the experimental retention time to the normalized retention time space used in the transition list. |
rt_extraction_window | The used retention time extraction window |
void pickExperiment | ( | MSExperiment< Peak1D > & | chromatograms, |
FeatureMap & | output, | ||
TargetedExperiment & | transition_exp, | ||
TransformationDescription | trafo, | ||
MSExperiment< Peak1D > & | swath_map | ||
) |
Picker and prepare functions.
Pick features in one experiment containing chromatogram
Function for for wrapping in Python, only uses OpenMS datastructures and does not return the map.
chromatograms | The input chromatograms |
output | The output features with corresponding scores |
transition_exp | The transition list describing the experiment |
trafo | Optional transformation of the experimental retention time to the normalized retention time space used in the transition list |
swath_map | Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted |
Referenced by OpenSwathWorkflow::RTNormalization().
void pickExperiment | ( | OpenSwath::SpectrumAccessPtr | input, |
FeatureMap & | output, | ||
OpenSwath::LightTargetedExperiment & | transition_exp, | ||
TransformationDescription | trafo, | ||
OpenSwath::SpectrumAccessPtr | swath_map, | ||
TransitionGroupMapType & | transition_group_map | ||
) |
Pick features in one experiment containing chromatogram.
input | The input chromatograms |
output | The output features with corresponding scores |
transition_exp | The transition list describing the experiment |
trafo | Optional transformation of the experimental retention time to the normalized retention time space used in the transition list. |
swath_map | Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available. |
transition_group_map | Output mapping of transition groups |
void prepareProteinPeptideMaps_ | ( | OpenSwath::LightTargetedExperiment & | transition_exp | ) |
Prepares the internal mappings of peptides and proteins.
Calling this method _is_ required before calling scorePeakgroups.
transition_exp | The transition list describing the experiment |
Referenced by OpenSwathWorkflow::scoreAllChromatograms().
void scorePeakgroups | ( | MRMTransitionGroupType & | transition_group, |
TransformationDescription & | trafo, | ||
OpenSwath::SpectrumAccessPtr | swath_map, | ||
FeatureMap & | output | ||
) |
Score all peak groups of a transition group.
Iterate through all features found along the chromatograms of the transition group and score each one individually.
transition_group | The MRMTransitionGroup to be scored (input) |
trafo | Optional transformation of the experimental retention time to the normalized retention time space used in the transition list. |
swath_map | Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available. |
output | The output features with corresponding scores (the found features will be added to this FeatureMap). |
Referenced by OpenSwathWorkflow::scoreAllChromatograms().
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inline |
Add an MS1 map containing spectra.
For DIA (SWATH-MS), an optional MS1 map can be supplied which can be used to extract precursor ion signal and provides additional scores. If no MS1 map is provided, the respective scores are not calculated.
ms1_map | The raw mass spectrometric MS1 data |
Referenced by OpenSwathWorkflow::scoreAllChromatograms().
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inline |
Set the flag for strict mapping.
Referenced by OpenSwathWorkflow::RTNormalization().
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privatevirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 12:49:28 using doxygen 1.8.11 |