Simple OpenSwathWorkflow to perform RT and m/z correction based on a set of known peptides. More...

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

Inheritance diagram for OpenSwathRetentionTimeNormalization:

Public Member Functions
TransformationDescription	performRTNormalization (const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const String &mz_correction_function, Size debug_level, bool sonar=false)
	Perform RT and m/z correction of the input data using RT-normalization peptides. 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...

Private Member Functions
TransformationDescription	RTNormalization (const TargetedExperiment &transition_exp_, const std::vector< OpenMS::MSChromatogram > &chromatograms, double min_rsq, double min_coverage, const Param &default_ffparam, const Param &irt_detection_param, std::vector< OpenSwath::SwathMap > &swath_maps, const String &mz_correction_function, double mz_extraction_window, bool ppm)
	Perform RT and m/z correction using the MRMFeatureFinderScoring. More...

void	simpleExtractChromatograms (const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram > &chromatograms, const ChromExtractParams &cp, bool sonar)
	Simple method to extract chromatograms (for the RT-normalization peptides) More...

Static Private Member Functions
static void	addChromatograms (MSChromatogram &base_chrom, const MSChromatogram &newchrom)

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

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

Simple OpenSwathWorkflow to perform RT and m/z correction based on a set of known peptides.

Member Function Documentation

◆ addChromatograms()

static void addChromatograms	(	MSChromatogram &	base_chrom,
		const MSChromatogram &	newchrom
	)

staticprivate

◆ performRTNormalization()

TransformationDescription performRTNormalization	(	const OpenMS::TargetedExperiment &	irt_transitions,
		std::vector< OpenSwath::SwathMap > &	swath_maps,
		double	min_rsq,
		double	min_coverage,
		const Param &	feature_finder_param,
		const ChromExtractParams &	cp_irt,
		const Param &	irt_detection_param,
		const String &	mz_correction_function,
		Size	debug_level,
		bool	sonar = `false`
	)

Perform RT and m/z correction of the input data using RT-normalization peptides.

This function extracts the RT normalization chromatograms and then uses the chromatograms to find features (in RTNormalization). If desired, also m/z correction is performed using the lock masses of the given peptides. Therefore, swath_maps may be changed in this function.

Parameters

irt_transitions	A set of transitions used for the RT normalization peptides
swath_maps	The raw data (swath maps)
min_rsq	Minimal R^2 value that is expected for the RT regression
min_coverage	Minimal coverage of the chromatographic space that needs to be achieved
feature_finder_param	Parameter set for the feature finding in chromatographic dimension
cp_irt	Parameter set for the chromatogram extraction
irt_detection_param	Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc)
mz_correction_function	If correction in m/z is desired, which function should be used
debug_level	Debug level (writes out the RT normalization chromatograms if larger than 1)

Referenced by SortPairDoubleByFirst().

◆ RTNormalization()

TransformationDescription RTNormalization	(	const TargetedExperiment &	transition_exp_,
		const std::vector< OpenMS::MSChromatogram > &	chromatograms,
		double	min_rsq,
		double	min_coverage,
		const Param &	default_ffparam,
		const Param &	irt_detection_param,
		std::vector< OpenSwath::SwathMap > &	swath_maps,
		const String &	mz_correction_function,
		double	mz_extraction_window,
		bool	ppm
	)

private

Perform RT and m/z correction using the MRMFeatureFinderScoring.

Parameters

transition_exp_	The transitions for the normalization peptides
chromatograms	The extracted chromatograms
min_rsq	Minimal R^2 value that is expected for the RT regression
min_coverage	Minimal coverage of the chromatographic space that needs to be achieved
feature_finder_param	Parameter set for the feature finding in chromatographic dimension
irt_detection_param	Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc)
swath_maps	The raw data for the m/z correction
mz_correction_function	If correction in m/z is desired, which function should be used

Note: : feature_finder_param are copied because they are changed here.; : This function is based on the algorithm inside the OpenSwathRTNormalizer tool

◆ simpleExtractChromatograms()

void simpleExtractChromatograms	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenMS::TargetedExperiment &	irt_transitions,
		std::vector< OpenMS::MSChromatogram > &	chromatograms,
		const ChromExtractParams &	cp,
		bool	sonar
	)

private

Simple method to extract chromatograms (for the RT-normalization peptides)

Public Member Functions

Private Member Functions