| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Private Attributes | List of all members
MultiplexClustering Class Reference

clusters results from multiplex filtering More...

`#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexClustering.h>`

Inheritance diagram for MultiplexClustering:

## Classes

class | MultiplexDistance
| scaled Euclidean distance for clustering More...

## Public Types

typedef GridBasedCluster::Point | Point
| cluster centre, cluster bounding box, grid index More...
Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...

## Public Member Functions

| MultiplexClustering (const MSExperiment &exp_profile, const MSExperiment &exp_picked, const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &boundaries, double rt_typical, double rt_minimum)
| constructor More...
| MultiplexClustering (const MSExperiment &exp, double mz_tolerance, bool mz_tolerance_unit, double rt_typical, double rt_minimum)
| constructor More...
std::vector< std::map< int, GridBasedCluster > > | cluster (const std::vector< MultiplexFilteredMSExperiment > &filter_results)
| cluster filter results Data points are grouped into clusters. Each cluster contains data about one peptide multiplet. More...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Private Attributes

std::vector< double > | grid_spacing_mz_
| grid spacing for clustering More...
std::vector< double > | grid_spacing_rt_
double | rt_scaling_
| scaling in y-direction for clustering More...
double | rt_typical_
| typical retention time More...
double | rt_minimum_
| minimum retention time More...

## Additional Inherited Members

Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. More...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

clusters results from multiplex filtering

The multiplex filtering algorithm identified regions in the picked and profile data that correspond to peptide features. This clustering algorithm takes these filter results as input and groups data points that belong to the same peptide features. It makes use of the general purpose hierarchical clustering implementation LocalClustering.

See also
  MultiplexFiltering
  LocalClustering

## Member Typedef Documentation

## ◆ Point

typedef GridBasedCluster::Point Point

cluster centre, cluster bounding box, grid index

DPosition<2>

## Constructor & Destructor Documentation

## ◆ MultiplexClustering() [1/2]

MultiplexClustering | ( | const MSExperiment & | exp_profile,
|  | const MSExperiment & | exp_picked,
|  | const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > & | boundaries,
|  | double | rt_typical,
|  | double | rt_minimum
| ) |  |

constructor

Parameters

  exp_profile | experimental data in profile mode
  exp_picked | experimental data in centroid mode
  boundaries | peak boundaries for exp_picked
  rt_typical | elution time of a characteristic peptide in the sample
  rt_minimum | shortest elution time i.e. all peptides appearing for a shorter time are being ignored

Exceptions

  Exception::IllegalArgument | if centroided data and the corresponding list of peak boundaries do not contain same number of spectra

## ◆ MultiplexClustering() [2/2]

MultiplexClustering | ( | const MSExperiment & | exp,
|  | double | mz_tolerance,
|  | bool | mz_tolerance_unit,
|  | double | rt_typical,
|  | double | rt_minimum
| ) |  |

constructor

Parameters

  exp | experimental data in centroid mode
  mz_tolerance | margin in m/z with which the centres of the same peak in different spectra my shift (or 'jitter')
  mz_tolerance_unit | unit for mz_tolerance, ppm (true), Da (false)
  rt_typical | elution time of a characteristic peptide in the sample
  rt_minimum | shortest elution time i.e. all peptides appearing for a shorter time are being ignored

Exceptions

  Exception::IllegalArgument | if centroided data and the corresponding list of peak boundaries do not contain same number of spectra

## Member Function Documentation

## ◆ cluster()

std::vector<std::map<int,GridBasedCluster> > cluster | ( | const std::vector< MultiplexFilteredMSExperiment > & | filter_results | ) |

cluster filter results Data points are grouped into clusters. Each cluster contains data about one peptide multiplet.

Parameters

  filter_results | data points relevant for peptide multiplets i.e. output from multiplex filtering

Returns
  cluster results (cluster ID, details about cluster including list of filter result IDs belonging to the cluster)

## Member Data Documentation

## ◆ grid_spacing_mz_

std::vector<double> grid_spacing_mz_

private

grid spacing for clustering

## ◆ grid_spacing_rt_

std::vector<double> grid_spacing_rt_

private

## ◆ rt_minimum_

double rt_minimum_

private

minimum retention time

## ◆ rt_scaling_

double rt_scaling_

private

scaling in y-direction for clustering

## ◆ rt_typical_

double rt_typical_

private

typical retention time