ExperimentalDesign Class Reference

Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class. More...

#include <OpenMS/METADATA/ExperimentalDesign.h>

Collaboration diagram for ExperimentalDesign:

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< String > >	getUniqueSampleRowToSampleMapping () const
std::map< String, 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< String, unsigned >	getSampleToConditionMapping () const
std::map< std::pair< String, unsigned >, unsigned >	getPathLabelToSampleMapping (bool use_basename_only) const
	return <file_path, label> to sample index 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
Size	filterByBasenames (const std::set< String > &bns)
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 an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class.

Experimental designs can be provided in two formats: the one-table format and the two-table format.

The one-table format is simpler but slightly more redundant.

The one-table format consists of mandatory (file columns) and optional sample metadata (sample columns).

The mandatory file columns are Fraction_Group, Fraction, Spectra_Filepath and Label. These columns capture the mapping of quantitative values to files for label-free and multiplexed experiments and enables fraction-aware data processing.

• Fraction_Group: a numeric identifier that indicates which fractions are grouped together. Please do NOT reuse the same identifiers across samples! Assign identifiers continuously.
• Fraction: a numeric identifier that indicates which fraction was measured in this file. In the case of unfractionated data, the fraction identifier is 1 for all samples. Make sure the same identifiers are used across different Fraction_Groups, as this determines which fractions correspond to each other.
• Label: a numeric identifier for the label. 1 for label-free, 1 and 2 for SILAC light/heavy, e.g., 1-10 for TMT10Plex
• Spectra_Filepath: a filename or path as string representation (e.g., SILAC_file.mzML)

For processing with MSstats, the optional sample columns are typically MSstats_Condition and MSstats_BioReplicate with an additional MSstats_Mixture column in the case of TMT labeling. They capture the experimental factors and conditions associated with a sample.

• MSstats_Condition: a string that indicates the condition (e.g., control or 1000 mMol). Will be forwarded to MSstats and can then be used to specify test contrasts.
• MSstats_BioReplicate: a string identifier to indicate biological replication of a sample. Entries with the same Sample/Condition/BioReplicate but different Filepath (and therefore FractionGroup number) will be treated as technical replicates.
• MSstats_Mixture: (for TMT labeling only): a string identifier to indicate the mixture of samples labeled with different TMT reagents, which can be analyzed in a single mass spectrometry experiment. E.g., same samples labeled with different TMT reagents have a different mixture identifier. Technical replicates need to have the same mixture identifier.

For details on the MSstats columns please refer to the MSstats manual for details (https://www.bioconductor.org/packages/release/bioc/vignettes/MSstats/inst/doc/MSstats.html).

Fraction_Group	Fraction	Spectra_Filepath	Label	MSstats_Condition	MSstats_BioReplicate
1	1	UPS1_12500amol_R1.mzML	1	12500 amol	1
2	1	UPS1_12500amol_R2.mzML	1	12500 amol	2
3	1	UPS1_12500amol_R3.mzML	1	12500 amol	3
...	...	...	...	...	...
22	1	UPS1_500amol_R1.mzML	1	500 amol	1
23	1	UPS1_500amol_R2.mzML	1	500 amol	2
24	1	UPS1_500amol_R3.mzML	1	500 amol	3

Alternatively, the experimental design can be specified with a file consisting of two tables whose headers are separated by a blank line. The two tables are:

• The file section table and the sample section table.
• The file section consists of columns Fraction_Group, Fraction, Spectra_Filepath, Label and Sample

The sample section consists of columns Sample, MSstats_Condition and MSstats_BioReplicate.

The content is the same as described for the one table format, except that the additional numeric sample column allows referencing between file and sample section.

Fraction_Group	Fraction	Spectra_Filepath	Label	Sample
1	1	UPS1_12500amol_R1.mzML	1	1
2	1	UPS1_12500amol_R2.mzML	1	2
...	...	...	...	...
22	1	UPS1_500amol_R1.mzML	1	22

Sample	MSstats_Condition	MSstats_BioReplicate
1	12500 amol	1
2	12500 amol	2
...	...	...
22	500 amol	3

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

filterByBasenames()

Size filterByBasenames

(

const std::set< String > &

bns

)

filters the MSFileSection to only include a given subset of files whose basenames are given with bns

Returns

number of files that have been filtered

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 index mapping

getSample()

unsigned getSample	(	unsigned	fraction_group,
		unsigned	label = 1
	)

getSampleSection()

const ExperimentalDesign::SampleSection& getSampleSection

(

)

const

getSampleToConditionMapping()

std::map<String, unsigned> getSampleToConditionMapping

(

)

const

return Sample name 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<String, 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<String> > getUniqueSampleRowToSampleMapping

(

)

const

returns a map from a sample section row to sample id for clustering 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