| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Private Member Functions | List of all members
FeatureGroupingAlgorithmQT Class Reference
Analysis » FeatureGrouping

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

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

Inheritance diagram for FeatureGroupingAlgorithmQT:

## Public Member Functions

| FeatureGroupingAlgorithmQT ()
| Default constructor. More...
| ~FeatureGroupingAlgorithmQT () override
| Destructor. More...
void | group (const std::vector< FeatureMap > &maps, ConsensusMap &out) override
| Applies the algorithm to feature maps. More...
void | group (const std::vector< ConsensusMap > &maps, ConsensusMap &out) override
| Applies the algorithm to consensus maps. More...
Public Member Functions inherited from FeatureGroupingAlgorithm
| FeatureGroupingAlgorithm ()
| Default constructor. More...
| ~FeatureGroupingAlgorithm () override
| Destructor. More...
void | transferSubelements (const std::vector< ConsensusMap > &maps, ConsensusMap &out) const
| Transfers subelements (grouped features) from input consensus maps to the result consensus map. 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 &param)
| 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 FeatureGroupingAlgorithm * | create ()
| Creates a new instance of this class (for Factory) More...
static String | getProductName ()
| Returns the product name (for the Factory) More...
Static Public Member Functions inherited from FeatureGroupingAlgorithm
static void | registerChildren ()
| Register all derived classes in this method. More...

## Private Member Functions

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

## Additional Inherited Members

Protected Member Functions inherited from FeatureGroupingAlgorithm
template<class MapType >
void | postprocess_ (const std::vector< MapType > &maps, ConsensusMap &out)
Protected Member Functions inherited from DefaultParamHandler
virtual void | updateMembers_ ()
| This method is used to update extra member variables at the end of the setParameters() method. More...
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. 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

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:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
use_identifications | string | false | true, false | Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).
nr_partitions | int | 100 | min: 1 | How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )
ignore_charge | string | false | true, false | false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state
ignore_adduct | string | true | true, false | true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts
distance_RT:max_difference | float | 100.0 | min: 0.0 | Never pair features with a larger RT distance (in seconds).
distance_RT:exponent | float | 1.0 | min: 0.0 | Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_RT:weight | float | 1.0 | min: 0.0 | Final RT distances are weighted by this factor
distance_MZ:max_difference | float | 0.3 | min: 0.0 | Never pair features with larger m/z distance (unit defined by 'unit')
distance_MZ:unit | string | Da | Da, ppm | Unit of the 'max_difference' parameter
distance_MZ:exponent | float | 2.0 | min: 0.0 | Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_MZ:weight | float | 1.0 | min: 0.0 | Final m/z distances are weighted by this factor
distance_intensity:exponent | float | 1.0 | min: 0.0 | Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
distance_intensity:weight | float | 0.0 | min: 0.0 | Final intensity distances are weighted by this factor
distance_intensity:log_transform | string | disabled | enabled, disabled | Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Constructor & Destructor Documentation

## ◆ FeatureGroupingAlgorithmQT() [1/2]

FeatureGroupingAlgorithmQT | ( |  | ) |

Default constructor.

## ◆ ~FeatureGroupingAlgorithmQT()

~FeatureGroupingAlgorithmQT | ( |  | ) |

override

Destructor.

## ◆ FeatureGroupingAlgorithmQT() [2/2]

FeatureGroupingAlgorithmQT | ( | const FeatureGroupingAlgorithmQT & |  | ) |

private

Copy constructor intentionally not implemented -> private.

## Member Function Documentation

## ◆ create()

static FeatureGroupingAlgorithm* create | ( |  | ) |

inline static

Creates a new instance of this class (for Factory)

## ◆ getProductName()

static String getProductName | ( |  | ) |

inline static

Returns the product name (for the Factory)

## ◆ group() [1/2]

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

override virtual

Applies the algorithm to feature maps.

Precondition
  The data ranges of the input maps have to be up-to-date (use FeatureMap::updateRanges).

Exceptions

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

Implements FeatureGroupingAlgorithm.

Referenced by UTILProteomicsLFQ::link_().

## ◆ group() [2/2]

void group | ( | const std::vector< ConsensusMap > & | maps,
|  | ConsensusMap & | out
| ) |  |

override virtual

Applies the algorithm to consensus maps.

Precondition
  The data ranges of the input maps have to be up-to-date (use ConsensusMap::updateRanges).

Exceptions

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

Reimplemented from FeatureGroupingAlgorithm.

## ◆ group_()

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

private

Applies the algorithm to feature or consensus maps.

Precondition
  The data ranges of the input maps have to be up-to-date (use MapType::updateRanges).

Exceptions

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

## ◆ operator=()

FeatureGroupingAlgorithmQT& operator= | ( | const FeatureGroupingAlgorithmQT & |  | ) |

private

Assignment operator intentionally not implemented -> private.