The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMTransitionGroupPicker.h>

Inheritance diagram for MRMTransitionGroupPicker:

Public Types
typedef MSSpectrum < ChromatogramPeak >	RichPeakChromatogram
Public Member Functions
template<typename SpectrumT , typename TransitionT >
void	pickTransitionGroup (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group)
void	pickChromatogram (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &smoothed_chrom, RichPeakChromatogram &picked_chrom)
	Finds peaks in a chromatogram and annotates left/right borders.
template<typename SpectrumT , typename TransitionT >
MRMFeature	createMRMFeature (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, std::vector< SpectrumT > &picked_chroms, int &chr_idx, int &peak_idx)
	Create feature from a vector of chromatograms and a specified peak.
template<typename SpectrumT >
void	remove_overlapping_features (std::vector< SpectrumT > &picked_chroms, double best_left, double best_right)
	Remove overlaping features that are within the current seed feature or overlap with it.
void	findLargestPeak (std::vector< RichPeakChromatogram > &picked_chroms, int &chr_idx, int &peak_idx)
	Find largest peak in a vector of chromatograms.


	MRMTransitionGroupPicker ()
	Constructor.
	~MRMTransitionGroupPicker ()
	Destructor.
Protected Member Functions
double	calculateBgEstimation_ (const RichPeakChromatogram &smoothed_chromat, double best_left, double best_right)
	Will use the smoothed chromatograms.
void	updateMembers_ ()
	Synchronize members with param class.
MRMTransitionGroupPicker &	operator= (const MRMTransitionGroupPicker &rhs)
	Assignment operator is private for algorithm.
Resampling methods

template<typename SpectrumT , typename TransitionT >
void	prepareMasterContainer_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, SpectrumT &master_peak_container, int chr_idx, double best_left, double best_right)
	create an empty master peak container that has the correct mz / RT values set
template<typename SpectrumT >
SpectrumT	resampleChromatogram_ (const SpectrumT &chromatogram, SpectrumT &master_peak_container, double best_left, double best_right)
	use the master container from above to resample a chromatogram at those points stored in the master container
Protected Attributes
UInt	sgolay_frame_length_
UInt	sgolay_polynomial_order_
DoubleReal	gauss_width_
bool	use_gauss_
String	background_subtraction_
DoubleReal	peak_width_
DoubleReal	signal_to_noise_
DoubleReal	sn_win_len_
UInt	sn_bin_count_
int	stop_after_feature_
DoubleReal	stop_after_intensity_ratio_
std::vector< RichPeakChromatogram >	picked_chroms_
std::vector< RichPeakChromatogram >	smoothed_chroms_

Detailed Description

The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors.

It is called through pickTransitionGroup which will accept an MRMTransitionGroup filled with n chromatograms and perform the following steps:

Step 1: find features (peaks) in individual chromatograms
Step 2: merge these features to consensus features that span multiple chromatograms

Step 1 is performed by smoothing the individual chromatogram and applying the PeakPickerHiRes.

Step 2 is performed by finding the largest peak overall and use this to create a feature, propagating this through all chromatograms.

Member Typedef Documentation

typedef MSSpectrum<ChromatogramPeak> RichPeakChromatogram

Constructor & Destructor Documentation

MRMTransitionGroupPicker ( )

Constructor.

~MRMTransitionGroupPicker ( )

Destructor.

Member Function Documentation

double calculateBgEstimation_	(	const RichPeakChromatogram &	smoothed_chromat,
		double	best_left,
		double	best_right
	)			`[protected]`

Will use the smoothed chromatograms.

MRMFeature createMRMFeature	(	MRMTransitionGroup< SpectrumT, TransitionT > &	transition_group,
		std::vector< SpectrumT > &	picked_chroms,
		int &	chr_idx,
		int &	peak_idx
	)			`[inline]`

Create feature from a vector of chromatograms and a specified peak.

References MRMFeature::addFeature(), MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms(), Feature::getConvexHulls(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitionGroupID(), OpenMS::Constants::k, ConvexHull2D::setHullPoints(), Peak2D::setIntensity(), MetaInfoInterface::setMetaValue(), Peak2D::setMZ(), Feature::setOverallQuality(), Feature::setQuality(), and Peak2D::setRT().

void findLargestPeak	(	std::vector< RichPeakChromatogram > &	picked_chroms,
		int &	chr_idx,
		int &	peak_idx
	)

Find largest peak in a vector of chromatograms.

MRMTransitionGroupPicker& operator= ( const MRMTransitionGroupPicker & rhs ) [protected]

Assignment operator is private for algorithm.

void pickChromatogram	(	const RichPeakChromatogram &	chromatogram,
		RichPeakChromatogram &	smoothed_chrom,
		RichPeakChromatogram &	picked_chrom
	)

Finds peaks in a chromatogram and annotates left/right borders.

void pickTransitionGroup ( MRMTransitionGroup< SpectrumT, TransitionT > & transition_group ) [inline]

This function will accept a MRMTransitionGroup with raw chromatograms, create features on it and add the features back to the MRMTransitionGroup.

References MRMTransitionGroup< SpectrumType, TransitionType >::addFeature(), MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms(), Peak2D::getIntensity(), MetaInfoInterface::getMetaValue(), MSSpectrum< PeakT >::isSorted(), OpenMS::Constants::k, MSSpectrum< PeakT >::sortByIntensity(), and MSSpectrum< PeakT >::sortByPosition().

Referenced by MRMFeatureFinderScoring::pickExperiment().

void prepareMasterContainer_	(	MRMTransitionGroup< SpectrumT, TransitionT > &	transition_group,
		SpectrumT &	master_peak_container,
		int	chr_idx,
		double	best_left,
		double	best_right
	)			`[inline, protected]`

create an empty master peak container that has the correct mz / RT values set

References MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms().

void remove_overlapping_features	(	std::vector< SpectrumT > &	picked_chroms,
		double	best_left,
		double	best_right
	)			`[inline]`

Remove overlaping features that are within the current seed feature or overlap with it.

References OpenMS::Constants::k, and Peak2D::setIntensity().

SpectrumT resampleChromatogram_	(	const SpectrumT &	chromatogram,
		SpectrumT &	master_peak_container,
		double	best_left,
		double	best_right
	)			`[inline, protected]`