FalseDiscoveryRate

class pyopenms.FalseDiscoveryRate

Bases: object

Cython implementation of _FalseDiscoveryRate

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

__init__(self) → None

Methods

__init__(self)
apply	Overload:
applyBasic	Overload:
applyEstimated(self, ids)
applyEvaluateProteinIDs	Overload:
applyPickedProteinFDR(self, id, ...)
getDefaults(self)	Returns the default parameters
getName(self)	Returns the name
getParameters(self)	Returns the parameters
getSubsections(self)
rocN	Overload:
setName(self, in_0)	Sets the name
setParameters(self, param)	Sets the parameters

apply()

Overload:

apply(self, forward_ids: List[PeptideIdentification], reverse_ids: List[PeptideIdentification]) → None

Overload:

apply(self, id: List[PeptideIdentification]) → None

Overload:

apply(self, forward_ids: List[ProteinIdentification], reverse_ids: List[ProteinIdentification]) → None

Overload:

apply(self, id: List[ProteinIdentification]) → None

applyBasic()

Overload:

applyBasic(self, run_info: List[ProteinIdentification], ids: List[PeptideIdentification]) → None

Overload:

applyBasic(self, ids: List[PeptideIdentification], higher_score_better: bool, charge: int, identifier: bytes | str | String, only_best_per_pep: bool) → None

Overload:

applyBasic(self, cmap: ConsensusMap, use_unassigned_peptides: bool) → None

Overload:

applyBasic(self, id: ProteinIdentification, groups_too: bool) → None

applyEstimated(self, ids: List[ProteinIdentification]) → None

applyEvaluateProteinIDs()

Overload:

applyEvaluateProteinIDs(self, ids: List[ProteinIdentification], pepCutoff: float, fpCutoff: int, diffWeight: float) → float

Overload:

applyEvaluateProteinIDs(self, ids: ProteinIdentification, pepCutoff: float, fpCutoff: int, diffWeight: float) → float

applyPickedProteinFDR(self, id: ProteinIdentification, decoy_string: String, decoy_prefix: bool, groups_too: bool) → None

getDefaults(self) → Param

Returns the default parameters

getName(self) → bytes | str | String

Returns the name

getParameters(self) → Param

Returns the parameters

getSubsections(self) → List[bytes]

rocN()

Overload:

rocN(self, ids: List[PeptideIdentification], fp_cutoff: int) → float

Overload:

rocN(self, ids: ConsensusMap, fp_cutoff: int, include_unassigned_peptides: bool) → float

Overload:

rocN(self, ids: ConsensusMap, fp_cutoff: int, identifier: bytes | str | String, include_unassigned_peptides: bool) → float

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

Sets the name

setParameters(self, param: Param) → None

Sets the parameters