| OpenMS 2.5.0

Classes | Public Member Functions | Private Types | Private Member Functions | Static Private Member Functions | Static Private Attributes | List of all members
MSstatsFile Class Reference
Format » File IO

File adapter for MzTab files. More...

`#include <OpenMS/FORMAT/MSstatsFile.h>`

## Classes

struct | AggregatedConsensusInfo
class | MSstatsLine_
class | MSstatsTMTLine_

## Public Member Functions

| MSstatsFile ()=default
| Default constructor. More...
| ~MSstatsFile ()=default
| Destructor. More...
void | storeLFQ (const String &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const bool is_isotope_label_type, const String &bioreplicate, const String &condition, const String &retention_time_summarization_method)
| store label free experiment (MSstats) More...
void | storeISO (const String &filename, const ConsensusMap &consensus_map, const ExperimentalDesign &design, const StringList &reannotate_filenames, const String &bioreplicate, const String &condition, const String &mixture, const String &retention_time_summarization_method)
| store isobaric experiment (MSstatsTMT) More...

## 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< 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 String &retention_time_summarization_method, const bool rt_summarization_manual, TextFile &csv_out, const std::set< String > &peptideseq_quantifyable, LineType &peptideseq_to_prefix_to_intensities) const
bool | isQuantifyable_ (const std::set< String > &accs, const std::unordered_map< String, const IndProtGrp *> &accession_to_group) const

## Static Private Member Functions

static void | checkConditionLFQ_ (const ExperimentalDesign::SampleSection &sampleSection, const String &bioreplicate, const String &condition)
static void | checkConditionISO_ (const ExperimentalDesign::SampleSection &sampleSection, const String &bioreplicate, const String &condition, const String &mixture)
static void | assembleRunMap_ (std::map< std::pair< String, unsigned >, unsigned > &run_map, const ExperimentalDesign &design)
static bool | checkUnorderedContent_ (const std::vector< String > &first, const std::vector< String > &second)
static std::unordered_map< OpenMS::String, const IndProtGrp *> | getAccessionToGroupMap_ (const IndProtGrps &ind_prots)

## Static Private Attributes

static const String | na_string_
static const char | delim_ = ','
static const char | accdelim_ = ';'
static const char | quote_ = '"'

## Detailed Description

File adapter for MzTab files.

## Class Documentation

## ◆ OpenMS::MSstatsFile::AggregatedConsensusInfo

struct OpenMS::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< String > & | spectra_paths
| ) |  |

private

## ◆ assembleRunMap_()

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

static private

## ◆ checkConditionISO_()

static void checkConditionISO_ | ( | const ExperimentalDesign::SampleSection & | sampleSection,
|  | const String & | bioreplicate,
|  | const String & | condition,
|  | const String & | mixture
| ) |  |

static private

## ◆ checkConditionLFQ_()

static void checkConditionLFQ_ | ( | const ExperimentalDesign::SampleSection & | sampleSection,
|  | const String & | bioreplicate,
|  | const String & | condition
| ) |  |

static private

## ◆ checkUnorderedContent_()

static bool checkUnorderedContent_ | ( | const std::vector< String > & | first,
|  | const std::vector< String > & | second
| ) |  |

static private

## ◆ constructFile_()

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

private

## ◆ getAccessionToGroupMap_()

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

static private

## ◆ isQuantifyable_()

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

private

## ◆ meanIntensity_()

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

inline private

## ◆ storeISO()

void storeISO | ( | const String & | filename,
|  | const ConsensusMap & | consensus_map,
|  | const ExperimentalDesign & | design,
|  | const StringList & | reannotate_filenames,
|  | const String & | bioreplicate,
|  | const String & | condition,
|  | const String & | mixture,
|  | const String & | retention_time_summarization_method
| ) |  |

store isobaric experiment (MSstatsTMT)

## ◆ storeLFQ()

void storeLFQ | ( | const String & | filename,
|  | const ConsensusMap & | consensus_map,
|  | const ExperimentalDesign & | design,
|  | const StringList & | reannotate_filenames,
|  | const bool | is_isotope_label_type,
|  | const String & | bioreplicate,
|  | const String & | condition,
|  | const String & | retention_time_summarization_method
| ) |  |

store label free experiment (MSstats)

Referenced by UTILProteomicsLFQ::main_().

## ◆ sumIntensity_()

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

inline private

## Member Data Documentation

## ◆ accdelim_

const char accdelim_ = ';'

static private

## ◆ delim_

const char delim_ = ','

static private

## ◆ na_string_

const String na_string_

static private

## ◆ quote_

const char quote_ = '"'

static private