OpenMS
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File adapter for MSstats 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_ = '"' |
File adapter for MSstats files.
struct OpenMS::MSstatsFile::AggregatedConsensusInfo |
Class Members | ||
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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 |
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Default constructor.
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Destructor.
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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 | ||
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store isobaric experiment (MSstatsTMT)
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)
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