A map feature grouping algorithm for labeling techniques with two labels. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmLabeled.h>
Inheritance diagram for FeatureGroupingAlgorithmLabeled:
Public Member Functions | |
| FeatureGroupingAlgorithmLabeled () | |
| Default constructor. | |
| virtual | ~FeatureGroupingAlgorithmLabeled () |
| Destructor. | |
| virtual void | group (const std::vector< FeatureMap<> > &maps, ConsensusMap &out) |
| Applies the algorithm. | |
Static Public Member Functions | |
| static FeatureGroupingAlgorithm * | create () |
| Creates a new instance of this class (for Factory). | |
| static String | getProductName () |
| Returns the product name (for the Factory). | |
Private Member Functions | |
| FeatureGroupingAlgorithmLabeled (const FeatureGroupingAlgorithmLabeled &) | |
| Copy constructor is not implemented -> private. | |
| FeatureGroupingAlgorithmLabeled & | operator= (const FeatureGroupingAlgorithmLabeled &) |
| Assignment operator is not implemented -> private. | |
Detailed Description
A map feature grouping algorithm for labeling techniques with two labels.
It takes one maps and searches for corresponding features with a defined distance in RT and m/z.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| rt_estimate | string | true | true, false | If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance. |
| rt_pair_dist | float | -20 | optimal pair distance in RT [sec] from light to heavy feature | |
| rt_dev_low | float | 15 | min: 0 | maximum allowed deviation below optimal retention time distance |
| rt_dev_high | float | 15 | min: 0 | maximum allowed deviation above optimal retention time distance |
| mz_pair_dists | float list | [4] | optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge) | |
| mz_dev | float | 0.05 | min: 0 | maximum allowed deviation from optimal m/z distance |
| mrm | string | false | true, false | this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account) |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
Default constructor.
| virtual ~FeatureGroupingAlgorithmLabeled | ( | ) | [virtual] |
Destructor.
| FeatureGroupingAlgorithmLabeled | ( | const FeatureGroupingAlgorithmLabeled & | ) | [private] |
Copy constructor is not implemented -> private.
Member Function Documentation
| static FeatureGroupingAlgorithm* create | ( | ) | [inline, static] |
Creates a new instance of this class (for Factory).
| virtual void group | ( | const std::vector< FeatureMap<> > & | maps, | |
| ConsensusMap & | out | |||
| ) | [virtual] |
Applies the algorithm.
- Note:
- Exactly one input map has to be provided.
- The output map has to have two file descriptions, containing the same file name. The file descriptions have to be labeled 'heavy' and 'light'.
- Exceptions:
-
Exception::IllegalArgument is thrown if the input data is not valid.
Implements FeatureGroupingAlgorithm.
| FeatureGroupingAlgorithmLabeled& operator= | ( | const FeatureGroupingAlgorithmLabeled & | ) | [private] |
Assignment operator is not implemented -> private.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |