PeptideAndProteinQuant#
- class pyopenms.PeptideAndProteinQuant#
Bases:
object
Cython implementation of _PeptideAndProteinQuant
- Original C++ documentation is available here
– Inherits from [‘DefaultParamHandler’]
- __init__()#
Overload:
- __init__(self) None
Helper class for peptide and protein quantification based on feature data annotated with IDs
Overload:
- __init__(self, in_0: PeptideAndProteinQuant) None
Methods
Overload:
getDefaults
(self)Returns the default parameters
getName
(self)Returns the name
getParameters
(self)Returns the parameters
getStatistics
(self)getSubsections
(self)quantifyPeptides
(self, peptides)Compute peptide abundances
quantifyProteins
(self, proteins)Compute protein abundances
Overload:
setName
(self, in_0)Sets the name
setParameters
(self, param)Sets the parameters
- getStatistics(self) PeptideAndProteinQuant_Statistics #
- getSubsections(self) List[bytes] #
- quantifyPeptides(self, peptides: List[PeptideIdentification]) None #
Compute peptide abundances
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(self, proteins: ProteinIdentification) None #
Compute protein abundances
Peptide abundances must be computed first with quantifyPeptides(). Optional protein inference information (e.g. from Fido or ProteinProphet) can be supplied via proteins
- readQuantData()#
Overload:
- readQuantData(self, map_in: FeatureMap, ed: ExperimentalDesign) None
Read quantitative data from a feature map
Parameters should be set before using this method, as setting parameters will clear all results
Overload:
- readQuantData(self, map_in: ConsensusMap, ed: ExperimentalDesign) None
Read quantitative data from a consensus map
Parameters should be set before using this method, as setting parameters will clear all results
Overload:
- readQuantData(self, proteins: List[ProteinIdentification], peptides: List[PeptideIdentification], ed: ExperimentalDesign) None
Read quantitative data from identification results (for quantification via spectral counting)
Parameters should be set before using this method, as setting parameters will clear all results