OpenMS  2.5.0
Public Member Functions | Protected Member Functions | List of all members
UTILProteomicsLFQ Class Reference
Inheritance diagram for UTILProteomicsLFQ:
TOPPBase

Public Member Functions

 UTILProteomicsLFQ ()
 

Protected Member Functions

void registerOptionsAndFlags_ () override
 
map< String, String > mapMzML2Ids_ (StringList &in, StringList &in_ids)
 
map< String, String > mapId2MzMLs_ (const map< String, String > &m2i)
 
ExitCodes centroidAndCorrectPrecursors_ (const String &mz_file, MSExperiment &ms_centroided)
 
void recalibrateMasses_ (MSExperiment &ms_centroided, vector< PeptideIdentification > &peptide_ids, const String &id_file_abs_path)
 
double estimateMedianChromatographicFWHM_ (MSExperiment &ms_centroided)
 
void calculateSeeds_ (const MSExperiment &ms_centroided, FeatureMap &seeds, double median_fwhm)
 
double align_ (vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations)
 
void transform_ (vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations)
 
void link_ (vector< FeatureMap > &feature_maps, double median_fwhm, double max_alignment_diff, ConsensusMap &consensus_fraction)
 
double alignAndLink_ (vector< FeatureMap > &feature_maps, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, const double median_fwhm)
 
map< pair< String, UInt >, vector< int > > getPeptideOccurrence_ (const ConsensusMap &cons)
 
multimap< Size, PeptideIdentification > transferIDsBetweenSameFraction_ (const ConsensusMap &consensus_fraction, Size min_occurrence=3)
 
ExitCodes quantifyFraction_ (const pair< unsigned int, std::vector< String > > &ms_files, const map< String, String > &mzfile2idfile, double median_fwhm, const multimap< Size, PeptideIdentification > &transfered_ids, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, double &max_alignment_diff, set< String > &fixed_modifications, set< String > &variable_modifications)
 
ExitCodes main_ (int, const char **) override
 

Constructor & Destructor Documentation

◆ UTILProteomicsLFQ()

UTILProteomicsLFQ ( )
inline

Member Function Documentation

◆ align_()

double align_ ( vector< FeatureMap > &  feature_maps,
vector< TransformationDescription > &  transformations 
)
inlineprotected

◆ alignAndLink_()

double alignAndLink_ ( vector< FeatureMap > &  feature_maps,
ConsensusMap &  consensus_fraction,
vector< TransformationDescription > &  transformations,
const double  median_fwhm 
)
inlineprotected

◆ calculateSeeds_()

void calculateSeeds_ ( const MSExperiment &  ms_centroided,
FeatureMap &  seeds,
double  median_fwhm 
)
inlineprotected

◆ centroidAndCorrectPrecursors_()

ExitCodes centroidAndCorrectPrecursors_ ( const String &  mz_file,
MSExperiment &  ms_centroided 
)
inlineprotected

◆ estimateMedianChromatographicFWHM_()

double estimateMedianChromatographicFWHM_ ( MSExperiment &  ms_centroided)
inlineprotected

◆ getPeptideOccurrence_()

map<pair<String, UInt>, vector<int> > getPeptideOccurrence_ ( const ConsensusMap &  cons)
inlineprotected

◆ link_()

void link_ ( vector< FeatureMap > &  feature_maps,
double  median_fwhm,
double  max_alignment_diff,
ConsensusMap &  consensus_fraction 
)
inlineprotected

◆ main_()

ExitCodes main_ ( int  ,
const char **   
)
inlineoverrideprotected

◆ mapId2MzMLs_()

map<String, String> mapId2MzMLs_ ( const map< String, String > &  m2i)
inlineprotected

◆ mapMzML2Ids_()

map<String, String> mapMzML2Ids_ ( StringList &  in,
StringList &  in_ids 
)
inlineprotected

◆ quantifyFraction_()

ExitCodes quantifyFraction_ ( const pair< unsigned int, std::vector< String > > &  ms_files,
const map< String, String > &  mzfile2idfile,
double  median_fwhm,
const multimap< Size, PeptideIdentification > &  transfered_ids,
ConsensusMap &  consensus_fraction,
vector< TransformationDescription > &  transformations,
double &  max_alignment_diff,
set< String > &  fixed_modifications,
set< String > &  variable_modifications 
)
inlineprotected

◆ recalibrateMasses_()

void recalibrateMasses_ ( MSExperiment &  ms_centroided,
vector< PeptideIdentification > &  peptide_ids,
const String &  id_file_abs_path 
)
inlineprotected

◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )
inlineoverrideprotected

TODO: think about export of quality control files (qcML?)

◆ transferIDsBetweenSameFraction_()

multimap<Size, PeptideIdentification> transferIDsBetweenSameFraction_ ( const ConsensusMap &  consensus_fraction,
Size  min_occurrence = 3 
)
inlineprotected

◆ transform_()

void transform_ ( vector< FeatureMap > &  feature_maps,
vector< TransformationDescription > &  transformations 
)
inlineprotected