MapAlignmentAlgorithmKD Class Reference

An efficient reference-free feature map alignment algorithm for unlabeled data. More...

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

Collaboration diagram for MapAlignmentAlgorithmKD:

Public Member Functions
	MapAlignmentAlgorithmKD (Size num_maps, const Param &param)
	Constructor. More...
virtual	~MapAlignmentAlgorithmKD ()
	Default destructor. More...
void	addRTFitData (const KDTreeFeatureMaps &kd_data)
	Compute data points needed for RT transformation in the current kd_data, add to fit_data_. More...
void	fitLOWESS ()
	Fit LOWESS to fit_data_, store final models in transformations_. More...
void	transform (KDTreeFeatureMaps &kd_data) const
	Transform RTs for kd_data. More...

Protected Member Functions
virtual void	updateMembers_ ()
Size	computeCCs_ (const KDTreeFeatureMaps &kd_data, std::vector< Size > &cc_index) const
	Compute connected components, store CC indices in member cc_index. Return number of CCs. More...
void	getCCs_ (const KDTreeFeatureMaps &kd_data, std::map< Size, std::vector< Size > > &result) const
	Return connected components. More...
void	filterCCs_ (const KDTreeFeatureMaps &kd_data, const std::map< Size, std::vector< Size > > &ccs, std::map< Size, std::vector< Size > > &filtered_ccs) const
	Filter connected components (return conflict-free CCs of sufficiently large size and small diameter) More...

Private Member Functions
	MapAlignmentAlgorithmKD ()
	Default constructor is not supposed to be used. More...

Private Attributes
std::vector< TransformationModel::DataPoints >	fit_data_
	RT data for fitting the LOWESS. More...
std::vector< TransformationModelLowess * >	transformations_
	LOWESS transformations. More...
Param	param_
	Parameters. More...
double	max_pairwise_log_fc_
	Maximum absolute log10 fold change threshold between compatible features. More...
double	rt_tol_secs_
	RT tolerance. More...
double	mz_tol_
	m/z tolerance More...
bool	mz_ppm_
	m/z unit ppm? More...

Detailed Description

An efficient reference-free feature map alignment algorithm for unlabeled data.

This algorithm uses a kd-tree to efficiently compute conflict-free connected components (CCC) in a compatibility graph on feature data. This graph is comprised of nodes corresponding to features and edges connecting features f and f' iff both are within each other's tolerance windows (wrt. RT and m/z difference). CCCs are those CCs that do not contain multiple features from the same input map, and whose features all have the same charge state.

All CCCs above a user-specified minimum size are considered true sets of corresponding features and based on these, LOWESS transformations are computed for each input map such that the average deviation from the mean retention time within all CCCs is minimized.

Constructor & Destructor Documentation

MapAlignmentAlgorithmKD() [1/2]

MapAlignmentAlgorithmKD	(	Size	num_maps,
		const Param &	param
	)

Constructor.

~MapAlignmentAlgorithmKD()

virtual ~MapAlignmentAlgorithmKD ( )

virtual

Default destructor.

MapAlignmentAlgorithmKD() [2/2]

MapAlignmentAlgorithmKD ( )

private

Default constructor is not supposed to be used.

Member Function Documentation

addRTFitData()

void addRTFitData

(

const KDTreeFeatureMaps &

kd_data

)

Compute data points needed for RT transformation in the current kd_data, add to fit_data_.

computeCCs_()

Size computeCCs_ ( const KDTreeFeatureMaps &  kd_data, std::vector< Size > &  cc_index  ) const

protected

Compute connected components, store CC indices in member cc_index. Return number of CCs.

filterCCs_()

void filterCCs_ ( const KDTreeFeatureMaps &  kd_data, const std::map< Size, std::vector< Size > > &  ccs, std::map< Size, std::vector< Size > > &  filtered_ccs  ) const

protected

Filter connected components (return conflict-free CCs of sufficiently large size and small diameter)

fitLOWESS()

void fitLOWESS

(

)

Fit LOWESS to fit_data_, store final models in transformations_.

getCCs_()

void getCCs_ ( const KDTreeFeatureMaps &  kd_data, std::map< Size, std::vector< Size > > &  result  ) const

protected

Return connected components.

transform()

void transform

(

KDTreeFeatureMaps &

kd_data

)

const

Transform RTs for kd_data.

updateMembers_()

virtual void updateMembers_ ( )

protectedvirtual

Member Data Documentation

fit_data_

std::vector<TransformationModel::DataPoints> fit_data_

private

RT data for fitting the LOWESS.

max_pairwise_log_fc_

double max_pairwise_log_fc_

private

Maximum absolute log10 fold change threshold between compatible features.

mz_ppm_

bool mz_ppm_

private

m/z unit ppm?

mz_tol_

double mz_tol_

private

m/z tolerance

param_

Param param_

private

Parameters.

rt_tol_secs_

double rt_tol_secs_

private

RT tolerance.

transformations_

std::vector<TransformationModelLowess*> transformations_

private

LOWESS transformations.