regvelo.metrics.cellfate_perturbation

regvelo.metrics.cellfate_perturbation(perturbed, baseline, terminal_state=None, terminal_indices=None, method='likelihood', solver='gmres')[source]

Compute depletion likelihood or score for TF perturbation.

Parameters:

  • perturbed (dict[str, AnnData]) – Dictionary mapping TF candidate names to their perturbed AnnData objects, each containing precomputed fate probabilities under obsm["lineages_fwd"].

  • baseline (AnnData) – Unperturbed AnnData object with precomputed fate probabilities under obsm["lineages_fwd"].

  • terminal_state (Union[str, Sequence[str], None]) – One or more terminal states for which depletion scores are computed.

  • terminal_indices (Optional[dict[str, list[str]]]) – Dictionary mapping each terminal state to the list of cell indices (obs_names) belonging to it.

  • method (Literal['likelihood', 't-statistics']) – Scoring method to use: - “t-statistics”: uses t-statistics. - “likelihood”: uses ROC AUC score.

  • solver (Union[str, Literal['direct', 'gmres', 'lgmres', 'bicgstab', 'gcrotmk']]) – Linear system solver used by CellRank’s GPCCA estimator when computing fate probabilities. Supported options include: - “direct”: direct solver. - “gmres”: Generalized Minimal Residual method (default). - “lgmres”: Loose GMRES. - “bicgstab”: BiConjugate Gradient Stabilized method. - “gcrotmk”: GCROTMK solver. Choice of solver may affect performance and numerical stability.

Return type:

DataFrame

Returns:

: DataFrame summarizing depletion scores and significance statistics.