Implements the isotope wavelet feature finder. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmIsotopeWavelet.h>
Inheritance diagram for FeatureFinderAlgorithmIsotopeWavelet:
Classes | |
| struct | BoxElement |
| Internally used data structure for the sweep line algorithm. More... | |
Public Types | |
| typedef FeatureFinderAlgorithm | Base |
| typedef Peak1D | PeakType |
 Public Types inherited from FeatureFinderAlgorithm | |
| typedef PeakMap | MapType |
| Input map type. More... | |
| typedef MapType::CoordinateType | CoordinateType |
| Coordinate/Position type of peaks. More... | |
| typedef MapType::IntensityType | IntensityType |
| Intensity type of peaks. More... | |
Public Member Functions | |
| FeatureFinderAlgorithmIsotopeWavelet () | |
| Default Constructor. More... | |
| virtual | ~FeatureFinderAlgorithmIsotopeWavelet () |
| Destructor. More... | |
| MSSpectrum * | createHRData (const UInt i) |
| void | run () |
| The working horse of this class. More... | |
| Public Member Functions inherited from FeatureFinderAlgorithm | |
| FeatureFinderAlgorithm () | |
| default constructor More... | |
| virtual | ~FeatureFinderAlgorithm () |
| destructor More... | |
| virtual Param | getDefaultParameters () const |
| Returns the default parameters. Reimplement. More... | |
| void | setData (const MapType &map, FeatureMap &features, FeatureFinder &ff) |
| Sets a reference to the calling FeatureFinder. More... | |
| virtual void | setSeeds (const FeatureMap &seeds) |
| Sets a reference to the calling FeatureFinder. 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... | |
Static Public Member Functions | |
| static const String | getProductName () |
| static FeatureFinderAlgorithm * | create () |
| Static Public Member Functions inherited from FeatureFinderAlgorithm | |
| static void | registerChildren () |
| register all derived classes here (see FeatureFinderAlgorithm_impl.h) More... | |
Protected Types | |
| typedef std::map< UInt, BoxElement > | Box |
| Key: RT (index), value: BoxElement. More... | |
Protected Member Functions | |
| void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. 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 | max_charge_ |
| The maximal charge state we will consider. More... | |
| double | intensity_threshold_ |
| The only parameter of the isotope wavelet. More... | |
| UInt | RT_votes_cutoff_ |
| UInt | real_RT_votes_cutoff_ |
| UInt | RT_interleave_ |
| The number of subsequent scans a pattern must cover in order to be considered as signal. More... | |
| String | use_gpus_ |
| String | intensity_type_ |
| bool | check_PPMs_ |
| bool | hr_data_ |
| std::vector< UInt > | gpu_ids_ |
| A list of all GPU devices that can be used. More... | |
| Int | progress_counter_ |
| Protected Attributes inherited from FeatureFinderAlgorithm | |
| const MapType * | map_ |
| Input data pointer. More... | |
| FeatureMap * | features_ |
| Output data pointer. More... | |
| FeatureFinder * | ff_ |
| Pointer to the calling FeatureFinder that is used to access the feature flags. 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... | |
Detailed Description
Implements the isotope wavelet feature finder.
The FeatureFinderAlgorithmIsotopeWavelet class has been designed for finding features in 1D or 2D MS data sets using the isotope wavelet. In the case of two dimensional data, the class provides additionally the sweep line algorithm. Please note that the algorithm implemented here is only marginally related to the algorithm presented in Schulz-Trieglaff et al. (2007, 2008), as no fitting procedure is applied anymore after the wavelet-based seeding step. The wavelet has been designed to extract even very lowly-abundant features (see Hussong et al. (2007, 2009)), usually featuring a very low signal-to-noise ratio. The wavelet in its current implementation is not able to resolve overlapping patterns (see also Hussong et al. (2009)) and slightly shifts masses to the right due to the construction of the wavelet.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| max_charge | int | 3 | min: 1 | The maximal charge state to be considered. |
| intensity_threshold | float | -1 | The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform. If you set intensity_threshold=-1, t' will be zero. As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g. |
|
| intensity_type | string | ref | ref, trans, corrected | Determines the intensity type returned for the identified features. 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet). |
| check_ppm | string | false | true, false | Enables/disables a ppm test vs. the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied. |
| hr_data | string | false | true, false | Must be true in case of high-resolution data, i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data, e.g.). Please check a single MS scan out of your recording, if you are unsure. |
| sweep_line:rt_votes_cutoff | int | 5 | min: 0 | Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature. |
| sweep_line:rt_interleave | int | 1 | min: 0 | Defines the maximum number of scans (w.r.t. rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Member Typedef Documentation
◆ Base
| typedef FeatureFinderAlgorithm Base |
◆ Box
|
protected |
Key: RT (index), value: BoxElement.
◆ PeakType
Constructor & Destructor Documentation
◆ FeatureFinderAlgorithmIsotopeWavelet()
Default Constructor.
◆ ~FeatureFinderAlgorithmIsotopeWavelet()
|
virtual |
Destructor.
Member Function Documentation
◆ create()
|
static |
◆ createHRData()
| MSSpectrum* createHRData | ( | const UInt | i | ) |
◆ getProductName()
|
static |
◆ run()
|
virtual |
The working horse of this class.
Implements FeatureFinderAlgorithm.
◆ updateMembers_()
|
protectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
Member Data Documentation
◆ check_PPMs_
|
protected |
◆ gpu_ids_
|
protected |
A list of all GPU devices that can be used.
◆ hr_data_
|
protected |
◆ intensity_threshold_
|
protected |
The only parameter of the isotope wavelet.
◆ intensity_type_
|
protected |
◆ max_charge_
|
protected |
The maximal charge state we will consider.
◆ progress_counter_
|
protected |
◆ real_RT_votes_cutoff_
|
protected |
◆ RT_interleave_
|
protected |
The number of subsequent scans a pattern must cover in order to be considered as signal.
◆ RT_votes_cutoff_
|
protected |
◆ use_gpus_
|
protected |