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template<typename SpectrumT , typename TransitionT > |
void | pickTransitionGroup (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group) |
| Pick a group of chromatograms belonging to the same peptide. More...
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template<typename SpectrumT , typename TransitionT > |
MRMFeature | createMRMFeature (const MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, std::vector< SpectrumT > &picked_chroms, const std::vector< SpectrumT > &smoothed_chroms, const int chr_idx, const int peak_idx) |
| Create feature from a vector of chromatograms and a specified peak. More...
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template<typename SpectrumT > |
void | remove_overlapping_features (std::vector< SpectrumT > &picked_chroms, double best_left, double best_right) |
| Remove overlapping features. More...
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void | findLargestPeak (const std::vector< MSChromatogram > &picked_chroms, int &chr_idx, int &peak_idx) |
| Find largest peak in a vector of chromatograms. More...
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void | findWidestPeakIndices (const std::vector< MSChromatogram > &picked_chroms, Int &chrom_idx, Int &point_idx) const |
| Given a vector of chromatograms, find the indices of the chromatogram containing the widest peak and of the position of highest intensity. More...
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| MRMTransitionGroupPicker () |
| Constructor. More...
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| ~MRMTransitionGroupPicker () override |
| Destructor. More...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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void | updateMembers_ () override |
| Synchronize members with param class. More...
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MRMTransitionGroupPicker & | operator= (const MRMTransitionGroupPicker &rhs) |
| Assignment operator is protected for algorithm. More...
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template<typename SpectrumT , typename TransitionT > |
const SpectrumT & | selectChromHelper_ (const MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, const String &native_id) |
| Select matching precursor or fragment ion chromatogram. More...
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template<typename SpectrumT , typename TransitionT > |
double | computeQuality_ (const MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, const std::vector< SpectrumT > &picked_chroms, const int chr_idx, const double best_left, const double best_right, String &outlier) |
| Compute transition group quality (higher score is better) More...
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template<typename SpectrumT > |
void | recalculatePeakBorders_ (const std::vector< SpectrumT > &picked_chroms, double &best_left, double &best_right, double max_z) |
| Recalculate the borders of the peak. More...
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template<typename SpectrumT > |
void | prepareMasterContainer_ (const SpectrumT &ref_chromatogram, SpectrumT &master_peak_container, double left_boundary, double right_boundary) |
| Create an empty master peak container that has the correct mz / RT values set. More...
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template<typename SpectrumT > |
SpectrumT | resampleChromatogram_ (const SpectrumT &chromatogram, const SpectrumT &master_peak_container, double left_boundary, double right_boundary) |
| Resample a container at the positions indicated by the master peak container. More...
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Protected Member Functions inherited from DefaultParamHandler |
void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More...
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The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors.
It is called through pickTransitionGroup which will accept an MRMTransitionGroup filled with n chromatograms and perform the following steps:
- Step 1: find features (peaks) in individual chromatograms
- Step 2: merge these features to consensus features that span multiple chromatograms
Step 1 is performed by smoothing the individual chromatogram and applying the PeakPickerHiRes.
Step 2 is performed by finding the largest peak overall and use this to create a feature, propagating this through all chromatograms.
double computeQuality_ |
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const MRMTransitionGroup< SpectrumT, TransitionT > & |
transition_group, |
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const std::vector< SpectrumT > & |
picked_chroms, |
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const int |
chr_idx, |
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const double |
best_left, |
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const double |
best_right, |
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String & |
outlier |
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inlineprotected |
void pickTransitionGroup |
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MRMTransitionGroup< SpectrumT, TransitionT > & |
transition_group | ) |
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inline |
Pick a group of chromatograms belonging to the same peptide.
Will identify peaks in a set of chromatograms that belong to the same peptide. The chromatograms are given in the MRMTransitionGroup container which also contains the mapping of the chromatograms to their metadata. Only chromatograms from detecting transitions are used for peak picking. Identifying transitions will be processed alongside but do not contribute to the meta-data, e.g. total_xic or peak_apices_sum.
The resulting features are added to the MRMTransitionGroup. Each feature contains the following meta-data:
- PeptideRef
- leftWidth
- rightWidth
- total_xic (fragment trace XIC sum)
- peak_apices_sum
References MRMTransitionGroup< ChromatogramType, TransitionType >::addFeature(), MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogramIdsMatch(), MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatograms(), Peak2D::getIntensity(), MetaInfoInterface::getMetaValue(), ChromatogramSettings::getNativeID(), MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatograms(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitions(), MRMTransitionGroup< ChromatogramType, TransitionType >::hasTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent(), OpenMS::Constants::k, OPENMS_PRECONDITION, and MSChromatogram::sortByIntensity().
void recalculatePeakBorders_ |
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const std::vector< SpectrumT > & |
picked_chroms, |
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double & |
best_left, |
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double & |
best_right, |
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double |
max_z |
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inlineprotected |
Recalculate the borders of the peak.
By collecting all left and right borders of contained peaks, a consensus peak is computed. By looking at the means and standard deviations of all the peak borders it is estimated whether the proposed peak border deviates too much from the consensus one. If the deviation is too high (in this case), then we fall back to the "consensus" (a median here).
References OpenMS::Constants::k, LOG_DEBUG, and OpenMS::Math::mean().
void remove_overlapping_features |
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std::vector< SpectrumT > & |
picked_chroms, |
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double |
best_left, |
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double |
best_right |
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inline |
Remove overlapping features.
Remove features that are within the current seed (between best_left and best_right) or overlap with it. An overlapping feature is defined as a feature that has either of its borders within the border of the current peak
Directly adjacent features are allowed, e.g. they can share one border.
References OpenMS::Constants::k.