Representation of the Experimental Design in OpenMS. Instances can be loaded via the ExperimentalDesignFile class. More...

#include <OpenMS/METADATA/ExperimentalDesign.h>

Classes
class	MSFileSectionEntry

class	SampleSection

Public Types
using	MSFileSection = std::vector< MSFileSectionEntry >

Public Member Functions
	ExperimentalDesign ()=default

	ExperimentalDesign (const MSFileSection &msfile_section, const SampleSection &sample_section)

const MSFileSection &	getMSFileSection () const

void	setMSFileSection (const MSFileSection &msfile_section)

const ExperimentalDesign::SampleSection &	getSampleSection () const

void	setSampleSection (const SampleSection &sample_section)

std::map< std::vector< String >, std::set< unsigned > >	getUniqueSampleRowToSampleMapping () const

std::map< unsigned, unsigned >	getSampleToPrefractionationMapping () const

std::map< unsigned int, std::vector< String > >	getFractionToMSFilesMapping () const
	return fraction index to file paths (ordered by fraction_group) More...

std::vector< std::vector< std::pair< String, unsigned > > >	getConditionToPathLabelVector () const

std::map< std::vector< String >, std::set< unsigned > >	getConditionToSampleMapping () const
	return a condition (unique combination of sample section values except replicate) to Sample index mapping More...

std::map< std::pair< String, unsigned >, unsigned >	getPathLabelToPrefractionationMapping (bool use_basename_only) const

std::map< std::pair< String, unsigned >, unsigned >	getPathLabelToConditionMapping (bool use_basename_only) const

std::map< unsigned, unsigned >	getSampleToConditionMapping () const

std::map< std::pair< String, unsigned >, unsigned >	getPathLabelToSampleMapping (bool use_basename_only) const
	return <file_path, label> to sample mapping More...

std::map< std::pair< String, unsigned >, unsigned >	getPathLabelToFractionMapping (bool use_basename_only) const
	return <file_path, label> to fraction mapping More...

std::map< std::pair< String, unsigned >, unsigned >	getPathLabelToFractionGroupMapping (bool use_basename_only) const
	return <file_path, label> to fraction_group mapping More...

unsigned	getNumberOfSamples () const

unsigned	getNumberOfFractions () const

unsigned	getNumberOfLabels () const

unsigned	getNumberOfMSFiles () const

unsigned	getNumberOfFractionGroups () const

unsigned	getSample (unsigned fraction_group, unsigned label=1)

bool	isFractionated () const

bool	sameNrOfMSFilesPerFraction () const

Static Public Member Functions
static ExperimentalDesign	fromConsensusMap (const ConsensusMap &c)
	Extract experimental design from consensus map. More...

static ExperimentalDesign	fromFeatureMap (const FeatureMap &f)
	Extract experimental design from feature map. More...

static ExperimentalDesign	fromIdentifications (const std::vector< ProteinIdentification > &proteins)
	Extract experimental design from identifications. More...

Private Member Functions
std::vector< String >	getFileNames_ (bool basename) const

std::vector< unsigned >	getLabels_ () const

std::vector< unsigned >	getFractions_ () const

std::map< std::pair< String, unsigned >, unsigned >	pathLabelMapper_ (bool, unsigned(*f)(const ExperimentalDesign::MSFileSectionEntry &)) const
	Generic Mapper (Path, Label) -> f(row) More...

void	sort_ ()

void	isValid_ ()

Static Private Member Functions
template<typename T >
static void	errorIfAlreadyExists (std::set< T > &container, T &item, const String &message)

Private Attributes
MSFileSection	msfile_section_

SampleSection	sample_section_

Detailed Description

Representation of the Experimental Design in OpenMS. Instances can be loaded via the ExperimentalDesignFile class.

The experimental design in OpenMS consists of two sections: 1. FileSection captures the mapping of quantitative values to files and, optionally, to samples. 2. SampleSection captures the experimental factors and conditions associated with a sample.

The FileSection is mandatory while the SampleSection is optional and only required for downstream analysis.

Details on the FileSection:

To unambiguously map a single quantitative value we need to define: a. the label (e.g., label = 2 in the case of a heavy peptide in a light/heavy experiment) b. which spectra file did produce the result (e.g., path = "/data/SILAC_file.mzML") c. which fraction the file corresponds to (e.g., fraction = 1) d. a fraction group identifier that groups fractions (e.g., fraction_group = 1) Note: in the case of label-free data, the fraction group identifier has the same cardinality as the sample identifier. (e.) optionally, the sample that has been measured (e.g., sample = 1)

This information is defined in the FileSection and enables fraction aware data processing.

Details on the SampleSection:

To map a sample to conditions / factors we need to define: a. the sample ( e.g., sample = 1) b. multiple columns containing conditions / factors

Member Typedef Documentation

◆ MSFileSection

using MSFileSection = std::vector<MSFileSectionEntry>

Constructor & Destructor Documentation

◆ ExperimentalDesign() [1/2]

ExperimentalDesign ( )

default

◆ ExperimentalDesign() [2/2]

ExperimentalDesign	(	const MSFileSection &	msfile_section,
		const SampleSection &	sample_section
	)

Member Function Documentation

◆ errorIfAlreadyExists()

static void errorIfAlreadyExists	(	std::set< T > &	container,
		T &	item,
		const String &	message
	)

staticprivate

◆ fromConsensusMap()

static ExperimentalDesign fromConsensusMap ( const ConsensusMap & c )

static

Extract experimental design from consensus map.

◆ fromFeatureMap()

static ExperimentalDesign fromFeatureMap ( const FeatureMap & f )

static

Extract experimental design from feature map.

◆ fromIdentifications()

static ExperimentalDesign fromIdentifications ( const std::vector< ProteinIdentification > & proteins )

static

Extract experimental design from identifications.

◆ getConditionToPathLabelVector()

std::vector<std::vector<std::pair<String, unsigned> > > getConditionToPathLabelVector ( ) const

return vector of filepath/label combinations that share the same conditions after removing replicate columns in the sample section (e.g. for merging across replicates)

◆ getConditionToSampleMapping()

std::map<std::vector<String>, std::set<unsigned> > getConditionToSampleMapping ( ) const

return a condition (unique combination of sample section values except replicate) to Sample index mapping

◆ getFileNames_()

std::vector< String > getFileNames_ ( bool basename ) const

private

◆ getFractions_()

std::vector<unsigned> getFractions_ ( ) const

private

◆ getFractionToMSFilesMapping()

std::map<unsigned int, std::vector<String> > getFractionToMSFilesMapping ( ) const

return fraction index to file paths (ordered by fraction_group)

◆ getLabels_()

std::vector<unsigned> getLabels_ ( ) const

private

◆ getMSFileSection()

const MSFileSection& getMSFileSection ( ) const

◆ getNumberOfFractionGroups()

unsigned getNumberOfFractionGroups ( ) const

◆ getNumberOfFractions()

unsigned getNumberOfFractions ( ) const

◆ getNumberOfLabels()

unsigned getNumberOfLabels ( ) const

◆ getNumberOfMSFiles()

unsigned getNumberOfMSFiles ( ) const

◆ getNumberOfSamples()

unsigned getNumberOfSamples ( ) const

◆ getPathLabelToConditionMapping()

std::map< std::pair< String, unsigned >, unsigned> getPathLabelToConditionMapping ( bool use_basename_only ) const

return <file_path, label> to condition mapping (a condition is a unique combination of all columns in the sample section, except for replicates.

◆ getPathLabelToFractionGroupMapping()

std::map< std::pair< String, unsigned >, unsigned> getPathLabelToFractionGroupMapping ( bool use_basename_only ) const

return <file_path, label> to fraction_group mapping

◆ getPathLabelToFractionMapping()

std::map< std::pair< String, unsigned >, unsigned> getPathLabelToFractionMapping ( bool use_basename_only ) const

return <file_path, label> to fraction mapping

◆ getPathLabelToPrefractionationMapping()

std::map< std::pair< String, unsigned >, unsigned> getPathLabelToPrefractionationMapping ( bool use_basename_only ) const

return <file_path, label> to prefractionation mapping (a prefractionation group is a unique combination of all columns in the sample section, except for replicates.

◆ getPathLabelToSampleMapping()

std::map< std::pair< String, unsigned >, unsigned> getPathLabelToSampleMapping ( bool use_basename_only ) const

return <file_path, label> to sample mapping

◆ getSample()

unsigned getSample	(	unsigned	fraction_group,
		unsigned	label = `1`
	)

◆ getSampleSection()

const ExperimentalDesign::SampleSection& getSampleSection ( ) const

◆ getSampleToConditionMapping()

std::map<unsigned, unsigned> getSampleToConditionMapping ( ) const

return Sample index to condition mapping (a condition is a unique combination of all columns in the sample section, except for replicates. Numbering of conditions is alphabetical due to map.

◆ getSampleToPrefractionationMapping()

std::map<unsigned, unsigned> getSampleToPrefractionationMapping ( ) const

uses getUniqueSampleRowToSampleMapping to get the reversed map mapping sample ID to a real unique sample

◆ getUniqueSampleRowToSampleMapping()

std::map<std::vector<String>, std::set<unsigned> > getUniqueSampleRowToSampleMapping ( ) const

returns a map from a sample section row to sample id to cluster duplicate sample rows (e.g. to find all fractions of the same "sample")

◆ isFractionated()

bool isFractionated ( ) const

Returns: whether we have a fractionated design

◆ isValid_()

void isValid_ ( )

private

◆ pathLabelMapper_()

std::map< std::pair< String, unsigned >, unsigned> pathLabelMapper_	(	bool	,
		unsigned(*)(const ExperimentalDesign::MSFileSectionEntry &)	f
	)		const

private

Generic Mapper (Path, Label) -> f(row)

◆ sameNrOfMSFilesPerFraction()

bool sameNrOfMSFilesPerFraction ( ) const

Returns: whether all fraction groups have the same number of fractions

◆ setMSFileSection()

void setMSFileSection ( const MSFileSection & msfile_section )

◆ setSampleSection()

void setSampleSection ( const SampleSection & sample_section )

◆ sort_()

void sort_ ( )

private

Member Data Documentation

◆ msfile_section_

MSFileSection msfile_section_

private

◆ sample_section_

SampleSection sample_section_

private

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ MSFileSection

Constructor & Destructor Documentation

◆ ExperimentalDesign() [1/2]

◆ ExperimentalDesign() [2/2]

Member Function Documentation

◆ errorIfAlreadyExists()

◆ fromConsensusMap()

◆ fromFeatureMap()

◆ fromIdentifications()

◆ getConditionToPathLabelVector()

◆ getConditionToSampleMapping()

◆ getFileNames_()

◆ getFractions_()

◆ getFractionToMSFilesMapping()

◆ getLabels_()

◆ getMSFileSection()

◆ getNumberOfFractionGroups()

◆ getNumberOfFractions()

◆ getNumberOfLabels()

◆ getNumberOfMSFiles()

◆ getNumberOfSamples()

◆ getPathLabelToConditionMapping()

◆ getPathLabelToFractionGroupMapping()

◆ getPathLabelToFractionMapping()

◆ getPathLabelToPrefractionationMapping()

◆ getPathLabelToSampleMapping()

◆ getSample()

◆ getSampleSection()

◆ getSampleToConditionMapping()

◆ getSampleToPrefractionationMapping()

◆ getUniqueSampleRowToSampleMapping()

◆ isFractionated()

◆ isValid_()

◆ pathLabelMapper_()

◆ sameNrOfMSFilesPerFraction()

◆ setMSFileSection()

◆ setSampleSection()

◆ sort_()

Member Data Documentation

◆ msfile_section_

◆ sample_section_