MSstatsFile Class Reference

File adapter for MSstats files. More...

#include <OpenMS/FORMAT/MSstatsFile.h>

Collaboration diagram for MSstatsFile:

Classes
struct	AggregatedConsensusInfo
class	MSstatsLine_
class	MSstatsTMTLine_

Public Member Functions
	MSstatsFile ()=default
	Default constructor.
	~MSstatsFile ()=default
	Destructor.
void	storeLFQ (const std::string &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const bool is_isotope_label_type, const std::string &bioreplicate, const std::string &condition, const std::string &retention_time_summarization_method, const bool remove_shared_peptides=true)
	Store label free experiment (MSstats)
void	storeISO (const std::string &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const std::string &bioreplicate, const std::string &condition, const std::string &mixture, const std::string &retention_time_summarization_method, const bool remove_shared_peptides=true)
	Store isobaric experiment (MSstatsTMT)

Private Types
typedef OpenMS::Peak2D::IntensityType	Intensity
typedef OpenMS::Peak2D::CoordinateType	Coordinate

Private Member Functions
MSstatsFile::AggregatedConsensusInfo	aggregateInfo_ (const ConsensusMap &consensus_map, const std::vector< std::string > &spectra_paths)
OpenMS::Peak2D::IntensityType	sumIntensity_ (const std::set< OpenMS::Peak2D::IntensityType > &intensities) const
OpenMS::Peak2D::IntensityType	meanIntensity_ (const std::set< OpenMS::Peak2D::IntensityType > &intensities) const
template<class LineType >
void	constructFile_ (const std::string &retention_time_summarization_method, const bool rt_summarization_manual, TextFile &csv_out, const std::set< std::string > &peptideseq_quantifyable, LineType &peptideseq_to_prefix_to_intensities) const
bool	isQuantifyable_ (const std::set< std::string > &accs, const std::unordered_map< std::string, const IndProtGrp * > &accession_to_group) const

Static Private Member Functions
static void	checkConditionLFQ_ (const ExperimentalDesign::SampleSection &sampleSection, const std::string &bioreplicate, const std::string &condition)
static void	checkConditionISO_ (const ExperimentalDesign::SampleSection &sampleSection, const std::string &bioreplicate, const std::string &condition, const std::string &mixture)
static void	assembleRunMap_ (std::map< std::pair< std::string, unsigned >, unsigned > &run_map, const ExperimentalDesign &design)
static bool	isSubsetOf_ (const std::vector< std::string > &first, const std::vector< std::string > &second)
static void	warnOnSubsetFiles_ (const std::vector< std::string > &spectra_paths, const std::vector< std::string > &design_filenames)
static std::unordered_map< std::string, const IndProtGrp * >	getAccessionToGroupMap_ (const IndProtGrps &ind_prots)

Static Private Attributes
static const std::string	na_string_
static const char	delim_ = ','
static const char	accdelim_ = ';'
static const char	quote_ = '"'

Detailed Description

File adapter for MSstats files.

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Class Documentation

OpenMS::MSstatsFile::AggregatedConsensusInfo

struct OpenMS::MSstatsFile::AggregatedConsensusInfo

Collaboration diagram for MSstatsFile::AggregatedConsensusInfo:

Class Members
vector< vector< string > >	consensus_feature_filenames
vector< vector< Intensity > >	consensus_feature_intensities
vector< vector< unsigned > >	consensus_feature_labels
vector< vector< Coordinate > >	consensus_feature_retention_times
vector< BaseFeature >	features

Member Typedef Documentation

Coordinate

typedef OpenMS::Peak2D::CoordinateType Coordinate

private

Intensity

typedef OpenMS::Peak2D::IntensityType Intensity

private

Constructor & Destructor Documentation

MSstatsFile()

MSstatsFile ( )

default

Default constructor.

~MSstatsFile()

~MSstatsFile ( )

default

Destructor.

Member Function Documentation

aggregateInfo_()

MSstatsFile::AggregatedConsensusInfo aggregateInfo_ ( const ConsensusMap &  consensus_map, const std::vector< std::string > &  spectra_paths  )

private

assembleRunMap_()

static void assembleRunMap_ ( std::map< std::pair< std::string, unsigned >, unsigned > &  run_map, const ExperimentalDesign &  design  )

staticprivate

checkConditionISO_()

static void checkConditionISO_ ( const ExperimentalDesign::SampleSection &  sampleSection, const std::string &  bioreplicate, const std::string &  condition, const std::string &  mixture  )

staticprivate

checkConditionLFQ_()

static void checkConditionLFQ_ ( const ExperimentalDesign::SampleSection &  sampleSection, const std::string &  bioreplicate, const std::string &  condition  )

staticprivate

constructFile_()

template<class LineType >

void constructFile_ ( const std::string &  retention_time_summarization_method, const bool  rt_summarization_manual, TextFile &  csv_out, const std::set< std::string > &  peptideseq_quantifyable, LineType &  peptideseq_to_prefix_to_intensities  ) const

private

getAccessionToGroupMap_()

static std::unordered_map< std::string, const IndProtGrp * > getAccessionToGroupMap_ ( const IndProtGrps &  ind_prots )

staticprivate

isQuantifyable_()

bool isQuantifyable_ ( const std::set< std::string > &  accs, const std::unordered_map< std::string, const IndProtGrp * > &  accession_to_group  ) const

private

isSubsetOf_()

static bool isSubsetOf_ ( const std::vector< std::string > &  first, const std::vector< std::string > &  second  )

staticprivate

meanIntensity_()

OpenMS::Peak2D::IntensityType meanIntensity_ ( const std::set< OpenMS::Peak2D::IntensityType > &  intensities ) const

inlineprivate

storeISO()

void storeISO	(	const std::string &	filename,
		const ConsensusMap &	consensus_map,
		const ExperimentalDesign &	design,
		const StringList &	reannotate_filenames,
		const std::string &	bioreplicate,
		const std::string &	condition,
		const std::string &	mixture,
		const std::string &	retention_time_summarization_method,
		const bool	remove_shared_peptides = true
	)

Store isobaric experiment (MSstatsTMT)

Parameters

[in]	filename	Output filename
[in]	consensus_map	ConsensusMap with quantification data
[in]	design	ExperimentalDesign file
[in]	reannotate_filenames	Optional filenames for reannotation
[in]	bioreplicate	Column name for biological replicate in design
[in]	condition	Column name for condition in design
[in]	mixture	Column name for mixture in design (used for TMT experiments)
[in]	retention_time_summarization_method	Method for RT summarization
[in]	remove_shared_peptides	If true, shared peptides mapping to multiple indistinguishable protein groups are removed (default)

storeLFQ()

void storeLFQ	(	const std::string &	filename,
		const ConsensusMap &	consensus_map,
		const ExperimentalDesign &	design,
		const StringList &	reannotate_filenames,
		const bool	is_isotope_label_type,
		const std::string &	bioreplicate,
		const std::string &	condition,
		const std::string &	retention_time_summarization_method,
		const bool	remove_shared_peptides = true
	)

Store label free experiment (MSstats)

Parameters

[in]	filename	Output filename
[in]	consensus_map	ConsensusMap with quantification data
[in]	design	ExperimentalDesign file
[in]	reannotate_filenames	Optional filenames for reannotation
[in]	is_isotope_label_type	If true, IsotopeLabelType is 'H', else 'L'
[in]	bioreplicate	Column name for biological replicate in design
[in]	condition	Column name for condition in design
[in]	retention_time_summarization_method	Method for RT summarization
[in]	remove_shared_peptides	If true, shared peptides mapping to multiple indistinguishable protein groups are removed (default)

sumIntensity_()

OpenMS::Peak2D::IntensityType sumIntensity_ ( const std::set< OpenMS::Peak2D::IntensityType > &  intensities ) const

inlineprivate

warnOnSubsetFiles_()

static void warnOnSubsetFiles_ ( const std::vector< std::string > &  spectra_paths, const std::vector< std::string > &  design_filenames  )

staticprivate

Member Data Documentation

accdelim_

const char accdelim_ = ';'

staticprivate

delim_

const char delim_ = ','

staticprivate

na_string_

const std::string na_string_

staticprivate

quote_

const char quote_ = '"'

staticprivate