The PeakPickerMRM finds peaks a single chromatogram. More...
#include <OpenMS/ANALYSIS/OPENSWATH/PeakPickerMRM.h>
Inheritance diagram for PeakPickerMRM:
Public Types | |
| typedef MSSpectrum< ChromatogramPeak > | RichPeakChromatogram |
Public Member Functions | |
| void | pickChromatogram (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom) |
| Finds peaks in a single chromatogram and annotates left/right borders. More... | |
| PeakPickerMRM () | |
| Constructor. More... | |
| ~PeakPickerMRM () | |
| Destructor. 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 | pickChromatogramCrawdad_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom) |
| void | pickChromatogram_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom) |
| void | integratePeaks_ (const RichPeakChromatogram &chromatogram) |
| Compute peak area (peak integration) More... | |
| Size | findClosestPeak_ (const RichPeakChromatogram &chromatogram, double target_rt, Size current_peak=0) |
| Helper function to find the closest peak in a chromatogram to "target_rt". More... | |
| void | removeOverlappingPeaks_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom) |
| Helper function to remove overlapping peaks in a single Chromatogram. More... | |
| void | updateMembers_ () |
| Synchronize members with param class. More... | |
| PeakPickerMRM & | operator= (const PeakPickerMRM &rhs) |
| Assignment operator is protected for algorithm. More... | |
| Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
| UInt | sgolay_frame_length_ |
| UInt | sgolay_polynomial_order_ |
| double | gauss_width_ |
| bool | use_gauss_ |
| bool | remove_overlapping_ |
| double | peak_width_ |
| double | signal_to_noise_ |
| double | sn_win_len_ |
| UInt | sn_bin_count_ |
| String | method_ |
| std::vector< double > | integrated_intensities_ |
| std::vector< int > | left_width_ |
| std::vector< int > | right_width_ |
| 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... | |
Detailed Description
The PeakPickerMRM finds peaks a single chromatogram.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| sgolay_frame_length | int | 15 | The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added. |
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| sgolay_polynomial_order | int | 3 | Order of the polynomial that is fitted. | |
| gauss_width | float | 50 | Gaussian width in seconds, estimated peak size. | |
| use_gauss | string | true | Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter) | |
| peak_width | float | 40 | Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off. | |
| signal_to_noise | float | 1 | min: 0 | Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured. |
| sn_win_len | float | 1000 | Signal to noise window length. | |
| sn_bin_count | int | 30 | Signal to noise bin count. | |
| remove_overlapping_peaks | string | false | false, true | Try to remove overlapping peaks during peak picking |
| method | string | legacy | legacy, corrected, crawdad | Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad). |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
It uses the PeakPickerHiRes internally to find interesting seed candidates. These candidates are then expanded and a right/left border of the peak is searched. Additionally, overlapping peaks can be removed.
Member Typedef Documentation
Constructor & Destructor Documentation
| PeakPickerMRM | ( | ) |
Constructor.
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Destructor.
Member Function Documentation
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Helper function to find the closest peak in a chromatogram to "target_rt".
The search will start from the index current_peak, so the function is assuming the closest peak is to the right of current_peak.
It will return the index of the closest peak in the chromatogram.
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Compute peak area (peak integration)
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Assignment operator is protected for algorithm.
| void pickChromatogram | ( | const RichPeakChromatogram & | chromatogram, |
| RichPeakChromatogram & | picked_chrom | ||
| ) |
Finds peaks in a single chromatogram and annotates left/right borders.
It uses a modified algorithm of the PeakPickerHiRes
This function will return a picked chromatogram
Referenced by MRMTransitionGroupPicker::pickTransitionGroup().
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Helper function to remove overlapping peaks in a single Chromatogram.
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Synchronize members with param class.
Reimplemented from DefaultParamHandler.
Member Data Documentation
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