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