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FeatureGroupingAlgorithmQT Class Reference
[FeatureGrouping]

A feature grouping algorithm for unlabeled data. More...

#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmQT.h>

Inheritance diagram for FeatureGroupingAlgorithmQT:
FeatureGroupingAlgorithm DefaultParamHandler

List of all members.

Public Member Functions

 FeatureGroupingAlgorithmQT ()
 Default constructor.
virtual ~FeatureGroupingAlgorithmQT ()
 Destructor.
virtual void group (const std::vector< FeatureMap<> > &maps, ConsensusMap &out)
 Applies the algorithm to feature maps

Exceptions:
IllegalArgument is thrown if less than two input maps are given.

virtual void group (const std::vector< ConsensusMap > &maps, ConsensusMap &out)
 Applies the algorithm to consensus maps

Exceptions:
IllegalArgument is thrown if less than two input maps are given.

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

 FeatureGroupingAlgorithmQT (const FeatureGroupingAlgorithmQT &)
 Copy constructor intentionally not implemented -> private.
FeatureGroupingAlgorithmQT & operator= (const FeatureGroupingAlgorithmQT &)
 Assignment operator intentionally not implemented -> private.
template<typename MapType >
void group_ (const std::vector< MapType > &maps, ConsensusMap &out)
 Applies the algorithm to feature or consensus maps

Exceptions:
IllegalArgument is thrown if less than two input maps are given.

Detailed Description

A feature grouping algorithm for unlabeled data.

The algorithm takes a number of feature or consensus maps and searches for corresponding (consensus) features across different maps. The maps have to be aligned (i.e. retention time distortions corrected, e.g. using one of the MapAlignmentAlgorithms), but small deviations are tolerated.

This particular algorithm accumulates the features from all input maps, then applies a variant of QT clustering to find groups of corresponding features. For more details, see QTClusterFinder.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
use_identifications stringfalse true, falseNever link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).
ignore_charge stringfalse true, falseCompare features normally even if their charge states are different
distance_RT:max_difference float100 min: 0Maximum allowed difference in RT in seconds
distance_RT:exponent float1 min: 0Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_RT:weight float1 min: 0RT distances are weighted by this factor
distance_MZ:max_difference float0.3 min: 0Maximum allowed difference in m/z (unit defined by 'unit')
distance_MZ:unit stringDa Da, ppmUnit of the 'max_difference' parameter
distance_MZ:exponent float2 min: 0Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_MZ:weight float1 min: 0m/z distances are weighted by this factor
distance_intensity:exponent float1 min: 0Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_intensity:weight float0 min: 0Distances based on relative intensity are weighted by this factor

Note:

Constructor & Destructor Documentation

FeatureGroupingAlgorithmQT (  ) 

Default constructor.

virtual ~FeatureGroupingAlgorithmQT (  )  [virtual]

Destructor.

FeatureGroupingAlgorithmQT ( const FeatureGroupingAlgorithmQT &   )  [private]

Copy constructor intentionally not implemented -> private.

Member Function Documentation

static FeatureGroupingAlgorithm* create (  )  [inline, static]

Creates a new instance of this class (for Factory).

static String getProductName (  )  [inline, static]

Returns the product name (for the Factory).

virtual void group ( const std::vector< ConsensusMap > &  maps,
ConsensusMap &  out 
) [virtual]

Applies the algorithm to consensus maps

Exceptions:
IllegalArgument is thrown if less than two input maps are given.

Reimplemented from FeatureGroupingAlgorithm.

virtual void group ( const std::vector< FeatureMap<> > &  maps,
ConsensusMap &  out 
) [virtual]

Applies the algorithm to feature maps

Exceptions:
IllegalArgument is thrown if less than two input maps are given.

Implements FeatureGroupingAlgorithm.

void group_ ( const std::vector< MapType > &  maps,
ConsensusMap &  out 
) [private]

Applies the algorithm to feature or consensus maps

Exceptions:
IllegalArgument is thrown if less than two input maps are given.

FeatureGroupingAlgorithmQT& operator= ( const FeatureGroupingAlgorithmQT &   )  [private]

Assignment operator intentionally not implemented -> private.

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1