The LabeledPairFinder allows the matching of labeled features (features with a fixed distance). More...

Inheritance diagram for LabeledPairFinder:

Public Member Functions
	LabeledPairFinder ()
	Default constructor.
virtual	~LabeledPairFinder ()
	Destructor.
virtual void	run (const std::vector< ConsensusMap > &input_maps, ConsensusMap &result_map)
	Run the algorithm.
Static Public Member Functions
static BaseGroupFinder *	create ()
	Returns an instance of this class.
static const String	getProductName ()
	Returns the name of this module.
Protected Member Functions
DoubleReal	PValue_ (DoubleReal x, DoubleReal m, DoubleReal sig1, DoubleReal sig2)
	return the p-value at position x for the bi-Gaussian distribution with mean `m` and standard deviation `sig1` (left) and `sig2` (right)
Private Member Functions
	LabeledPairFinder (const LabeledPairFinder &source)
	Copy constructor not implemented => private.
LabeledPairFinder &	operator= (const LabeledPairFinder &source)
	Assignment operator not implemented => private.

Detailed Description

The LabeledPairFinder allows the matching of labeled features (features with a fixed distance).

Finds feature pairs that have a defined distance in RT and m/z in the same map.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
rt_estimate	string	true	true, false	If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance.
rt_pair_dist	float	-20		optimal pair distance in RT [sec] from light to heavy feature
rt_dev_low	float	15	min: 0	maximum allowed deviation below optimal retention time distance
rt_dev_high	float	15	min: 0	maximum allowed deviation above optimal retention time distance
mz_pair_dists	float list	[4]		optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)
mz_dev	float	0.05	min: 0	maximum allowed deviation from optimal m/z distance
mrm	string	false	true, false	this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)

Note:

Implement support for labled MRM experiments, Q1 m/z value and charges. (Andreas)

Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)

Constructor & Destructor Documentation

LabeledPairFinder ( )

Default constructor.

virtual ~LabeledPairFinder ( ) [inline, virtual]

Destructor.

LabeledPairFinder ( const LabeledPairFinder & source ) [private]

Copy constructor not implemented => private.

static BaseGroupFinder* create ( ) [inline, static]

Returns an instance of this class.

static const String getProductName ( ) [inline, static]

Returns the name of this module.

LabeledPairFinder& operator= ( const LabeledPairFinder & source ) [private]

Assignment operator not implemented => private.

return the p-value at position x for the bi-Gaussian distribution with mean m and standard deviation sig1 (left) and sig2 (right)

virtual void run	(	const std::vector< ConsensusMap > &	input_maps,
		ConsensusMap &	result_map
	)			`[virtual]`

Run the algorithm.

Note:: Exactly one input map has to be provided.; The output map has to have two file descriptions, containing the same file name. The file descriptions have to be labeled 'heavy' and 'light'.

Exceptions:

Exception::IllegalArgument

is thrown if the input data is not valid.

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1