FalseDiscoveryRate#

class pyopenms.FalseDiscoveryRate(*args, **kwargs)#

Calculates false discovery rates (FDR) from identifications DefaultParamHandler

Attributes

`apply`	In/out compatibility (pyOpenMS 3.5 behaviour): a Python list passed as `ids`, `fwd_ids`, `rev_ids` is also updated in place with the returned contents.
`applyBasic`	Overloaded function.
`applyBasicPeptideLevel`	Overloaded function.
`applyEstimated`	Applies estimated FDR calculation on protein IDs
`applyEvaluateProteinIDs`
`applyPickedProteinFDR`
`getDefaults`	Returns the default parameters
`getName`	Returns the name
`getParameters`	Returns the parameters
`getSubsections`
`rocN`	Overloaded function.
`setName`	Sets the name
`setParameters`	Sets the parameters

apply#: In/out compatibility (pyOpenMS 3.5 behaviour): a Python list passed as ids, fwd_ids, rev_ids is also updated in place with the returned contents.

applyBasic#

Overloaded function.

applyBasic(self, ids: pyopenms._pyopenms_metadata.PeptideIdentificationList, higher_score_better: bool, charge: int = 0, identifier: str = '', only_best_per_pep: bool = False) -> None

Applies basic FDR calculation

applyBasic(self, run_info: collections.abc.Sequence[pyopenms._pyopenms_kernel.ProteinIdentification], ids: pyopenms._pyopenms_metadata.PeptideIdentificationList) -> None

Applies basic FDR calculation using run info

applyBasic(self, cmap: pyopenms._pyopenms_kernel.ConsensusMap, use_unassigned_peptides: bool = True) -> None

Applies basic FDR calculation on ConsensusMap

applyBasic(self, id: pyopenms._pyopenms_kernel.ProteinIdentification, groups_too: bool = True) -> None

Applies basic FDR calculation on protein level

applyBasicPeptideLevel#

Overloaded function.

applyBasicPeptideLevel(self, ids: pyopenms._pyopenms_metadata.PeptideIdentificationList) -> None

Applies basic peptide-level FDR calculation

applyBasicPeptideLevel(self, cmap: pyopenms._pyopenms_kernel.ConsensusMap, use_unassigned_peptides: bool = True) -> None

Applies basic peptide-level FDR calculation on ConsensusMap

applyEstimated#

Applies estimated FDR calculation on protein IDs

In/out compatibility (pyOpenMS 3.5 behaviour): a Python list passed as ids is also updated in place with the returned contents.

rocN#

Overloaded function.

rocN(self, ids: pyopenms._pyopenms_metadata.PeptideIdentificationList, fp_cutoff: int) -> float

Calculates the ROC-N value (AUC) for peptide IDs

rocN(self, ids: pyopenms._pyopenms_metadata.PeptideIdentificationList, fp_cutoff: int, identifier: str) -> float

Calculates the ROC-N value for a specific identifier