FeatureFinderAlgorithm for MRM experiments. More...

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

Inheritance diagram for FeatureFinderAlgorithmMRM< PeakType, FeatureType >:

Public Types
enum	{ RT = Peak2D::RT, MZ = Peak2D::MZ }
Type definitions

typedef FeatureFinderAlgorithm < PeakType, FeatureType > ::MapType	MapType
typedef MapType::SpectrumType	SpectrumType
typedef SpectrumType::FloatDataArrays	FloatDataArrays
Public Member Functions
	FeatureFinderAlgorithmMRM ()
	default constructor
virtual void	run ()
	Main method for actual FeatureFinder.
Static Public Member Functions
static FeatureFinderAlgorithm < PeakType, FeatureType > *	create ()
static const String	getProductName ()
Protected Member Functions
DoubleReal	fitRT_ (std::vector< PeakType > &rt_input_data, InterpolationModel *&model) const
virtual void	updateMembers_ ()

Detailed Description

template<class PeakType, class FeatureType>
class OpenMS::FeatureFinderAlgorithmMRM< PeakType, FeatureType >

FeatureFinderAlgorithm for MRM experiments.

Experimental classes:: This tool has not been tested thoroughly and might behave not as expected!

This very simple algorithm has mainly been tested on dated generated on an ABI/SCIEX QTrap 4000. Maybe this algorithm cannot be directly applied on data generated by other mass spectrometers.

Precursor m/z information (Q1) is stored in the "MZ" metavalue of each feature! The feature's m/z itself is the Q3's ion m/z.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
min_rt_distance	float	10	min: 0	Minimal distance of MRM features in seconds.
min_num_peaks_per_feature	int	5	min: 1	Minimal number of peaks which are needed for a single feature
min_signal_to_noise_ratio	float	2	min: 0	Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise.
write_debug_files	string	false	true, false	If set to true, for each feature a plot will be created, in the subdirectory 'debug'
resample_traces	string	false	true, false	If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension
write_debuginfo	string	false	true, false	If set to true, debug messages are written, the output can be somewhat lengthy.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Typedef Documentation

typedef SpectrumType::FloatDataArrays FloatDataArrays

typedef FeatureFinderAlgorithm<PeakType, FeatureType>::MapType MapType

typedef MapType::SpectrumType SpectrumType

Member Enumeration Documentation

anonymous enum

Enumerator:

RT
MZ

Constructor & Destructor Documentation

FeatureFinderAlgorithmMRM ( ) [inline]

default constructor

References StringList::create(), DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), Param::setMinFloat(), Param::setMinInt(), Param::setValidStrings(), and Param::setValue().

Referenced by FeatureFinderAlgorithmMRM< PeakType, FeatureType >::create().

Member Function Documentation

static FeatureFinderAlgorithm<PeakType, FeatureType>* create ( ) [inline, static]

References FeatureFinderAlgorithmMRM< PeakType, FeatureType >::FeatureFinderAlgorithmMRM().

DoubleReal fitRT_	(	std::vector< PeakType > &	rt_input_data,
		InterpolationModel *&	model
	)			const `[inline, protected]`

References EmgFitter1D::fit1d(), and DefaultParamHandler::setParameters().

Referenced by FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

static const String getProductName ( ) [inline, static]

virtual void run ( ) [inline, virtual]

Main method for actual FeatureFinder.

References ConvexHull2D::addPoints(), FeatureFinderAlgorithm< PeakType, FeatureType >::features_, FeatureFinderAlgorithm< PeakType, FeatureType >::ff_, GaussFilter::filter(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::fitRT_(), MSExperiment< PeakT, ChromatogramPeakT >::getChromatograms(), Feature::getConvexHulls(), InterpolationModel::getIntensity(), MetaInfoInterface::getMetaValue(), Peak2D::getMZ(), Feature::getOverallQuality(), DefaultParamHandler::getParameters(), Peak2D::getRT(), SignalToNoiseEstimator< Container >::getSignalToNoise(), Param::getValue(), SignalToNoiseEstimator< Container >::init(), FeatureFinderAlgorithm< PeakType, FeatureType >::map_, DefaultParamHandler::param_, LinearResampler::raster(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::RT, Peak2D::setIntensity(), Peak1D::setIntensity(), MetaInfoInterface::setMetaValue(), ProductModel< 2 >::setModel(), Feature::setModelDescription(), Peak2D::setMZ(), Peak1D::setMZ(), Feature::setOverallQuality(), DefaultParamHandler::setParameters(), Peak2D::setPosition(), ProgressLogger::setProgress(), Feature::setQuality(), Peak2D::setRT(), EmgModel::setSamples(), ProgressLogger::startProgress(), and DataValue::toBool().

virtual void updateMembers_ ( ) [inline, protected, virtual]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1

FeatureFinderAlgorithmMRM< PeakType, FeatureType > Class Template Reference [FeatureFinder]

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions