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OpenMS
2.4.0
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The MRMFeatureFinder finds and scores peaks of transitions that co-elute. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
Public Types | |
typedef OpenSwath::LightTransition | TransitionType |
Type definitions. More... | |
typedef OpenSwath::LightTargetedExperiment | TargetedExpType |
typedef OpenSwath::LightCompound | PeptideType |
typedef OpenSwath::LightProtein | ProteinType |
typedef OpenSwath::LightModification | ModificationType |
typedef MRMTransitionGroup< MSChromatogram, 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 () override | |
Destructor. More... | |
void | pickExperiment (PeakMap &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, PeakMap &swath_map) |
Picker and prepare functions. More... | |
void | pickExperiment (OpenSwath::SpectrumAccessPtr input, FeatureMap &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, std::vector< OpenSwath::SwathMap > swath_maps, TransitionGroupMapType &transition_group_map) |
Pick features in one experiment containing chromatogram. More... | |
void | prepareProteinPeptideMaps_ (const OpenSwath::LightTargetedExperiment &transition_exp) |
Prepares the internal mappings of peptides and proteins. More... | |
void | scorePeakgroups (MRMTransitionGroupType &transition_group, const TransformationDescription &trafo, const std::vector< OpenSwath::SwathMap > &swath_maps, FeatureMap &output, bool ms1only=false) |
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... | |
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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... | |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Private Member Functions | |
void | splitTransitionGroupsDetection_ (const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_detection) |
Splits combined transition groups into detection transition groups. More... | |
void | splitTransitionGroupsIdentification_ (const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_identification, MRMTransitionGroupType &transition_group_identification_decoy) |
Splits combined transition groups into identification transition groups. More... | |
OpenSwath_Scores | scoreIdentification_ (MRMTransitionGroupType &transition_group_identification, OpenSwathScoring &scorer, const size_t feature_idx, const std::vector< std::string > &native_ids_detection, const double sn_win_len_, const unsigned int sn_bin_count_, const double det_intensity_ratio_score, const double det_mi_ratio_score, bool write_log_messages, const std::vector< OpenSwath::SwathMap > &swath_maps) |
Provides scoring for target and decoy identification against detecting transitions. More... | |
void | updateMembers_ () override |
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::LightCompound PeptideType |
typedef OpenSwath::LightProtein ProteinType |
typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType |
Type definitions.
Constructor.
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override |
Destructor.
void mapExperimentToTransitionList | ( | OpenSwath::SpectrumAccessPtr | input, |
OpenSwath::LightTargetedExperiment & | transition_exp, | ||
TransitionGroupMapType & | transition_group_map, | ||
TransformationDescription | trafo, | ||
double | rt_extraction_window | ||
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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 | ( | OpenSwath::SpectrumAccessPtr | input, |
FeatureMap & | output, | ||
OpenSwath::LightTargetedExperiment & | transition_exp, | ||
TransformationDescription | trafo, | ||
std::vector< OpenSwath::SwathMap > | swath_maps, | ||
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 pickExperiment | ( | PeakMap & | chromatograms, |
FeatureMap & | output, | ||
TargetedExperiment & | transition_exp, | ||
TransformationDescription | trafo, | ||
PeakMap & | swath_map | ||
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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 |
void prepareProteinPeptideMaps_ | ( | const 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 |
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private |
Provides scoring for target and decoy identification against detecting transitions.
The function is used twice, for target and decoy identification transitions. The results are reported analogously to the ones for detecting transitions but must be stored separately.
transition_group | Containing all detecting, identifying transitions |
transition_group_identification | Containing all detecting and identifying transitions |
scorer | An instance of OpenSwathScoring |
feature_idx | The index of the current feature |
native_ids_detection | The native IDs of the detecting transitions |
sn_win_len_ | The signal to noise window length |
sn_bin_count_ | The signal to noise bin count |
det_intensity_ratio_score | The intensity score of the detection transitions for normalization |
det_mi_ratio_score | The MI score of the detection transitions for normalization |
write_log_messages | Whether to write signal to noise log messages @value a struct of type OpenSwath_Scores containing either target or decoy values |
void scorePeakgroups | ( | MRMTransitionGroupType & | transition_group, |
const TransformationDescription & | trafo, | ||
const std::vector< OpenSwath::SwathMap > & | swath_maps, | ||
FeatureMap & | output, | ||
bool | ms1only = false |
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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). |
ms1only | Whether to only do MS1 scoring and skip all MS2 scoring |
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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 |
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Set the flag for strict mapping.
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Splits combined transition groups into detection transition groups.
For standard assays, transition_group_detection is identical to transition_group and the others are empty.
transition_group | Containing all detecting, identifying transitions |
transition_group_detection | To be filled with detecting transitions |
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Splits combined transition groups into identification transition groups.
For standard assays, transition_group_identification is empty. When UIS scoring is enabled, it contains the corresponding identification transitions.
transition_group | Containing all detecting, identifying transitions |
transition_group_identification | To be filled with identifying transitions |
transition_group_identification_decoy | To be filled with identifying decoy transitions |
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Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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