OpenMS
MultiplexClustering Class Reference

clusters results from multiplex filtering More...

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

Inheritance diagram for MultiplexClustering:
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Collaboration diagram for MultiplexClustering:
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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)
 constructor More...
 
 MultiplexClustering (const MSExperiment &exp, double mz_tolerance, bool mz_tolerance_unit, double rt_typical)
 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...
 
virtual ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (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...
 

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_
 
ProgressLoggerImplcurrent_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

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 
)

constructor

Parameters
exp_profileexperimental data in profile mode
exp_pickedexperimental data in centroid mode
boundariespeak boundaries for exp_picked
rt_typicalelution time of a characteristic peptide in the sample
Exceptions
Exception::IllegalArgumentif 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 
)

constructor

Parameters
expexperimental data in centroid mode
mz_tolerancemargin in m/z with which the centres of the same peak in different spectra my shift (or 'jitter')
mz_tolerance_unitunit for mz_tolerance, ppm (true), Da (false)
rt_typicalelution time of a characteristic peptide in the sample
Exceptions
Exception::IllegalArgumentif 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_resultsdata 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_scaling_

double rt_scaling_
private

scaling in y-direction for clustering

◆ rt_typical_

double rt_typical_
private

typical retention time