FeatureFinderIdentificationAlgorithm

class pyopenms.FeatureFinderIdentificationAlgorithm

Bases: object

Cython implementation of _FeatureFinderIdentificationAlgorithm

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

Algorithm class for FeatureFinderIdentification

External IDs (peptides_ext, proteins_ext) may be empty, in which case no machine learning or FDR estimation will be performed. Optional seeds from e.g. untargeted FeatureFinders can be added with seeds. Results will be written to features . Caution: peptide IDs will be shrunk to best hit, FFid metavalues added and potential seed IDs added.

Usage:

__init__(self) → None

Methods

__init__(self)
getChromatograms(self)	Returns chromatogram data as MSExperiment
getDefaults(self)	Returns the default parameters
getLibrary(self)	Returns constructed assay library
getMSData(self)	Returns ms data as MSExperiment
getName(self)	Returns the name
getParameters(self)	Returns the parameters
getSubsections(self)
run	Overload:
runOnCandidates(self, features)	Run feature detection on identified features (e.g.
setMSData(self, in_0)	Sets ms data
setName(self, in_0)	Sets the name
setParameters(self, param)	Sets the parameters

getChromatograms(self) → MSExperiment

Returns chromatogram data as MSExperiment

getDefaults(self) → Param

Returns the default parameters

getLibrary(self) → TargetedExperiment

Returns constructed assay library

getMSData(self) → MSExperiment

Returns ms data as MSExperiment

getName(self) → bytes | str | String

Returns the name

getParameters(self) → Param

Returns the parameters

getSubsections(self) → List[bytes]

run()

Overload:

run(self, peptides: List[PeptideIdentification], proteins: List[ProteinIdentification], peptides_ext: List[PeptideIdentification], proteins_ext: List[ProteinIdentification], features: FeatureMap) → None

Run feature detection

Parameters:

• peptides – Vector of identified peptides

• proteins – Vector of identified proteins

• peptides_ext – Vector of external identified peptides, can be used to transfer ids from other runs

• proteins_ext – Vector of external identified proteins, can be used to transfer ids from other runs

• features – Feature detection results will be added here

Overload:

run(self, peptides: List[PeptideIdentification], proteins: List[ProteinIdentification], peptides_ext: List[PeptideIdentification], proteins_ext: List[ProteinIdentification], features: FeatureMap, seeds: FeatureMap) → None

Run feature detection

Parameters:

• peptides – Vector of identified peptides

• proteins – Vector of identified proteins

• peptides_ext – Vector of external identified peptides, can be used to transfer ids from other runs

• proteins_ext – Vector of external identified proteins, can be used to transfer ids from other runs

• features – Feature detection results will be added here

• seeds – Optional seeds for feature detection from e.g. untargeted FeatureFinders

Overload:

run(self, peptides: List[PeptideIdentification], proteins: List[ProteinIdentification], peptides_ext: List[PeptideIdentification], proteins_ext: List[ProteinIdentification], features: FeatureMap, seeds: FeatureMap, spectra_file: String) → None

Run feature detection

Parameters:

• peptides – Vector of identified peptides

• proteins – Vector of identified proteins

• peptides_ext – Vector of external identified peptides, can be used to transfer ids from other runs

• proteins_ext – Vector of external identified proteins, can be used to transfer ids from other runs

• features – Feature detection results will be added here

• seeds – Optional seeds for feature detection from e.g. untargeted FeatureFinders

• spectra_file – Path will be stored in features in case the MSExperiment has no proper primaryMSRunPath

runOnCandidates(self, features: FeatureMap) → None

Run feature detection on identified features (e.g. loaded from an IdXML file)

setMSData(self, in_0: MSExperiment) → None

Sets ms data

setName(self, in_0: bytes | str | String) → None

Sets the name

setParameters(self, param: Param) → None

Sets the parameters