PeptideAndProteinQuant

class pyopenms.PeptideAndProteinQuant

Bases: object

Cython implementation of _PeptideAndProteinQuant

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PeptideAndProteinQuant.html

– Inherits from [‘DefaultParamHandler’]

__init__()

  • Cython signature: void PeptideAndProteinQuant() Helper class for peptide and protein quantification based on feature data annotated with IDs

  • Cython signature: void PeptideAndProteinQuant(PeptideAndProteinQuant &)

Methods

__init__

  • Cython signature: void PeptideAndProteinQuant()

getDefaults

Cython signature: Param getDefaults() Returns the default parameters

getName

Cython signature: String getName() Returns the name

getParameters

Cython signature: Param getParameters() Returns the parameters

getStatistics

Cython signature: PeptideAndProteinQuant_Statistics getStatistics()

getSubsections

Cython signature: libcpp_vector[String] getSubsections()

quantifyPeptides

Cython signature: void quantifyPeptides(libcpp_vector[PeptideIdentification] & peptides)

quantifyProteins

Cython signature: void quantifyProteins(ProteinIdentification & proteins)

readQuantData

  • Cython signature: void readQuantData(FeatureMap & map_in, ExperimentalDesign & ed)

setName

Cython signature: void setName(const String &) Sets the name

setParameters

Cython signature: void setParameters(Param & param) Sets the parameters
getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getStatistics()

Cython signature: PeptideAndProteinQuant_Statistics getStatistics()

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

quantifyPeptides()

Cython signature: void quantifyPeptides(libcpp_vector[PeptideIdentification] & peptides)

Based on quantitative data for individual charge states (in member pep_quant_), overall abundances for peptides are computed (and stored again in pep_quant_) Quantitative data must first be read via readQuantData() Optional (peptide-level) protein inference information (e.g. from Fido or ProteinProphet) can be supplied via peptides. In that case, peptide-to-protein associations - the basis for protein-level quantification - will also be read from peptides!

quantifyProteins()

Cython signature: void quantifyProteins(ProteinIdentification & proteins)

Peptide abundances must be computed first with quantifyPeptides(). Optional protein inference information (e.g. from Fido or ProteinProphet) can be supplied via proteins

readQuantData()

  • Cython signature: void readQuantData(FeatureMap & map_in, ExperimentalDesign & ed)

Parameters should be set before using this method, as setting parameters will clear all results

  • Cython signature: void readQuantData(ConsensusMap & map_in, ExperimentalDesign & ed)

Parameters should be set before using this method, as setting parameters will clear all results

  • Cython signature: void readQuantData(libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] & peptides, ExperimentalDesign & ed)

Parameters should be set before using this method, as setting parameters will clear all results

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters