A map alignment algorithm based on peptide identifications from MS2 spectra. More...

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

Inheritance diagram for MapAlignmentAlgorithmIdentification:

Collaboration diagram for MapAlignmentAlgorithmIdentification:

Public Member Functions
	MapAlignmentAlgorithmIdentification ()
	Default constructor. More...

	~MapAlignmentAlgorithmIdentification () override
	Destructor. More...

template<typename DataType >
void	setReference (DataType &data)

template<typename DataType >
void	align (std::vector< DataType > &data, std::vector< TransformationDescription > &transformations, Int reference_index=-1)
	Align feature maps, consensus maps, peak maps, or peptide identifications. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Types
typedef std::map< String, DoubleList >	SeqToList
	Type to store retention times given for individual peptide sequences. More...

typedef std::map< String, double >	SeqToValue
	Type to store one representative retention time per peptide sequence. More...

Protected Member Functions
void	computeMedians_ (SeqToList &rt_data, SeqToValue &medians, bool sorted=false)
	Compute the median retention time for each peptide sequence. More...

bool	getRetentionTimes_ (std::vector< PeptideIdentification > &peptides, SeqToList &rt_data)
	Collect retention time data from peptide IDs. More...

bool	getRetentionTimes_ (IdentificationData &id_data, SeqToList &rt_data)
	Collect retention time data from spectrum matches. More...

bool	getRetentionTimes_ (PeakMap &experiment, SeqToList &rt_data)
	Collect retention time data from peptide IDs annotated to spectra. More...

template<typename MapType >
bool	getRetentionTimes_ (MapType &features, SeqToList &rt_data)
	Collect retention time data from peptide IDs contained in feature maps or consensus maps. More...

void	computeTransformations_ (std::vector< SeqToList > &rt_data, std::vector< TransformationDescription > &transforms, bool sorted=false)
	Compute retention time transformations from RT data grouped by peptide sequence. More...

void	checkParameters_ (const Size runs)
	Check that parameter values are valid. More...

void	getReference_ ()
	Get reference retention times. More...

IdentificationData::ScoreTypeRef	handleIdDataScoreType_ (const IdentificationData &id_data)
	Helper function to find/define the score type for processing IdentificationData. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
Int	reference_index_
	Index of input file to use as reference (if any) More...

SeqToValue	reference_
	Reference retention times (per peptide sequence) More...

Size	min_run_occur_
	Minimum number of runs a peptide must occur in. More...

bool	use_feature_rt_ {}
	Use feature RT instead of RT from best peptide ID in the feature? More...

bool	use_adducts_ {}
	Consider differently adducted IDs as different? More...

double	min_score_
	Minimum score to reach for a peptide to be considered. More...

bool	score_cutoff_ {}
	Actually use the above defined score_cutoff? Needed since it is hard to define a non-cutting score for a user. More...

String	score_type_
	Score type to use for filtering. More...

bool(*	better_ )(double, double) = [](double, double) {return true;}
	Score better? More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Private Member Functions
	MapAlignmentAlgorithmIdentification (const MapAlignmentAlgorithmIdentification &)
	Copy constructor intentionally not implemented -> private. More...

MapAlignmentAlgorithmIdentification &	operator= (const MapAlignmentAlgorithmIdentification &)
	Assignment operator intentionally not implemented -> private. More...

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

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

A map alignment algorithm based on peptide identifications from MS2 spectra.

PeptideIdentification instances are grouped by sequence of the respective best-scoring PeptideHit and retention time data is collected (PeptideIdentification::getRT()). ID groups with the same sequence in different maps represent points of correspondence between the maps and form the basis of the alignment. Only the best PSM per spectrum is considered as the correct identification.

Each map is aligned to a reference retention time scale. This time scale can either come from a reference file (reference parameter) or be computed as a consensus of the input maps (median retention times over all maps of the ID groups). The maps are then aligned to this scale as follows:
The median retention time of each ID group in a map is mapped to the reference retention time of this group. Cubic spline smoothing is used to convert this mapping to a smooth function. Retention times in the map are transformed to the consensus scale by applying this function.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
score_type	string			Name of the score type to use for ranking and filtering (.oms input only). If left empty, a score type is picked automatically.
score_cutoff	string	false	true, false	Use only IDs above a score cut-off (parameter 'min_score') for alignment?
min_score	float	0.05		If 'score_cutoff' is 'true': Minimum score for an ID to be considered. Unless you have very few runs or identifications, increase this value to focus on more informative peptides.
min_run_occur	int	2	min: 2	Minimum number of runs (incl. reference, if any) in which a peptide must occur to be used for the alignment. Unless you have very few runs or identifications, increase this value to focus on more informative peptides.
max_rt_shift	float	0.5	min: 0.0	Maximum realistic RT difference for a peptide (median per run vs. reference). Peptides with higher shifts (outliers) are not used to compute the alignment. If 0, no limit (disable filter); if > 1, the final value in seconds; if <= 1, taken as a fraction of the range of the reference RT scale.
use_unassigned_peptides	string	true	true, false	Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps? If 'false', only peptide IDs assigned to features will be used.
use_feature_rt	string	false	true, false	When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to. If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used. Precludes 'use_unassigned_peptides'.
use_adducts	string	true	true, false	If IDs contain adducts, treat differently adducted variants of the same molecule as different.

Note:

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

Member Typedef Documentation

◆ SeqToList

typedef std::map<String, DoubleList> SeqToList

protected

Type to store retention times given for individual peptide sequences.

◆ SeqToValue

typedef std::map<String, double> SeqToValue

protected

Type to store one representative retention time per peptide sequence.

Constructor & Destructor Documentation

◆ MapAlignmentAlgorithmIdentification() [1/2]

MapAlignmentAlgorithmIdentification ( )

Default constructor.

◆ ~MapAlignmentAlgorithmIdentification()

~MapAlignmentAlgorithmIdentification ( )

override

Destructor.

◆ MapAlignmentAlgorithmIdentification() [2/2]

MapAlignmentAlgorithmIdentification ( const MapAlignmentAlgorithmIdentification & )

private

Copy constructor intentionally not implemented -> private.

Member Function Documentation

◆ align()

void align	(	std::vector< DataType > &	data,
		std::vector< TransformationDescription > &	transformations,
		Int	reference_index = `-1`
	)

inline

Align feature maps, consensus maps, peak maps, or peptide identifications.

Parameters

data	Vector of input data (FeatureMap, ConsensusMap, PeakMap or `vector<PeptideIdentification>`) that should be aligned.
transformations	Vector of RT transformations that will be computed.
reference_index	Index in `data` of the reference to align to, if any

Exceptions

Exception::MissingInformation Not enough suitable RT data to perform alignment

◆ checkParameters_()

void checkParameters_ ( const Size runs )

protected

Check that parameter values are valid.

Currently only 'min_run_occur' is checked.

Parameters

runs	Number of runs (input files) to be aligned

◆ computeMedians_()

void computeMedians_	(	SeqToList &	rt_data,
		SeqToValue &	medians,
		bool	sorted = `false`
	)

protected

Compute the median retention time for each peptide sequence.

Parameters

rt_data	Lists of RT values for diff. peptide sequences (input, will be sorted)
medians	Median RT values for the peptide sequences (output)
sorted	Are RT lists already sorted?

Exceptions

Exception::IllegalArgument if the input list is empty

◆ computeTransformations_()

void computeTransformations_	(	std::vector< SeqToList > &	rt_data,
		std::vector< TransformationDescription > &	transforms,
		bool	sorted = `false`
	)

protected

Compute retention time transformations from RT data grouped by peptide sequence.

Parameters

rt_data	Lists of RT values for diff. peptide sequences, per dataset (input, will be sorted)
transforms	Resulting transformations, per dataset (output)
sorted	Are RT lists already sorted?

◆ getReference_()

void getReference_ ( )

protected

Get reference retention times.

If a reference file is supplied via the reference parameter, extract retention time information and store it in reference_.

◆ getRetentionTimes_() [1/4]

bool getRetentionTimes_	(	IdentificationData &	id_data,
		SeqToList &	rt_data
	)

protected

Collect retention time data from spectrum matches.

Parameters

id_data	Input identification data
rt_data	Lists of RT values for diff. spectrum matches (output)

Returns: Are the RTs already sorted? (Here: false)

◆ getRetentionTimes_() [2/4]

bool getRetentionTimes_	(	MapType &	features,
		SeqToList &	rt_data
	)

inlineprotected

Collect retention time data from peptide IDs contained in feature maps or consensus maps.

The following global flags (mutually exclusive) influence the processing:
Depending on use_unassigned_peptides, unassigned peptide IDs are used in addition to IDs annotated to features.
Depending on use_feature_rt, feature retention times are used instead of peptide retention times. Depending on score_cutoff and min_score, only peptide IDs with minimum score X are used. Higher score better is determined from the first PeptideID encountered. Make sure they are the same. This param is useless with use_feature_rt yet.

Parameters

features	Input features for RT data
rt_data	Lists of RT values for diff. peptide sequences (output)

Returns: Are the RTs already sorted? (Here: true)

References MSExperiment::begin(), and MSExperiment::end().

◆ getRetentionTimes_() [3/4]

bool getRetentionTimes_	(	PeakMap &	experiment,
		SeqToList &	rt_data
	)

protected

Collect retention time data from peptide IDs annotated to spectra.

Parameters

experiment	Input map for RT data
rt_data	Lists of RT values for diff. peptide sequences (output)

Returns: Are the RTs already sorted? (Here: false)

◆ getRetentionTimes_() [4/4]

bool getRetentionTimes_	(	std::vector< PeptideIdentification > &	peptides,
		SeqToList &	rt_data
	)

protected

Collect retention time data from peptide IDs.

Parameters

peptides	Input peptide IDs (lists of peptide hits will be sorted)
rt_data	Lists of RT values for diff. peptide sequences (output)

Returns: Are the RTs already sorted? (Here: false)

◆ handleIdDataScoreType_()

IdentificationData::ScoreTypeRef handleIdDataScoreType_ ( const IdentificationData & id_data )

protected

Helper function to find/define the score type for processing IdentificationData.

Returns: Reference to the score type denoted by algorithm parameter "score_type"

◆ operator=()

MapAlignmentAlgorithmIdentification& operator= ( const MapAlignmentAlgorithmIdentification & )

private

Assignment operator intentionally not implemented -> private.

◆ setReference()

void setReference ( DataType & data )

inline

Member Data Documentation

◆ better_

bool(* better_) (double, double) = [](double, double) {return true;}

protected

Score better?

◆ min_run_occur_

Size min_run_occur_

protected

Minimum number of runs a peptide must occur in.

◆ min_score_

double min_score_

protected

Minimum score to reach for a peptide to be considered.

◆ reference_

SeqToValue reference_

protected

Reference retention times (per peptide sequence)

◆ reference_index_

Int reference_index_

protected

Index of input file to use as reference (if any)

◆ score_cutoff_

bool score_cutoff_ {}

protected

Actually use the above defined score_cutoff? Needed since it is hard to define a non-cutting score for a user.

◆ score_type_

String score_type_

protected

Score type to use for filtering.

◆ use_adducts_

bool use_adducts_ {}

protected

Consider differently adducted IDs as different?

◆ use_feature_rt_

bool use_feature_rt_ {}

protected

Use feature RT instead of RT from best peptide ID in the feature?

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SeqToList

◆ SeqToValue

Constructor & Destructor Documentation

◆ MapAlignmentAlgorithmIdentification() [1/2]

◆ ~MapAlignmentAlgorithmIdentification()

◆ MapAlignmentAlgorithmIdentification() [2/2]

Member Function Documentation

◆ align()

◆ checkParameters_()

◆ computeMedians_()

◆ computeTransformations_()

◆ getReference_()

◆ getRetentionTimes_() [1/4]

◆ getRetentionTimes_() [2/4]

◆ getRetentionTimes_() [3/4]

◆ getRetentionTimes_() [4/4]

◆ handleIdDataScoreType_()

◆ operator=()

◆ setReference()

Member Data Documentation

◆ better_

◆ min_run_occur_

◆ min_score_

◆ reference_

◆ reference_index_

◆ score_cutoff_

◆ score_type_

◆ use_adducts_

◆ use_feature_rt_