moscot.problems.time.TemporalProblem.score_genes_for_marginals

TemporalProblem.score_genes_for_marginals(gene_set_proliferation=None, gene_set_apoptosis=None, proliferation_key='proliferation', apoptosis_key='apoptosis', **kwargs)

Compute gene scores to obtain prior knowledge about proliferation and apoptosis.

The gene scores can be used in estimate_marginals() to estimate the initial growth rates as suggested in [Schiebinger et al., 2019]

Parameters:

• gene_set_proliferation (Union[Literal['human', 'mouse'], Sequence[str], None]) – Set of proliferation marker genes. If a str, it should correspond to the organism in proliferation_markers().

• gene_set_apoptosis (Union[Literal['human', 'mouse'], Sequence[str], None]) – Set of apoptosis marker genes. If a str, it should correspond to the organism in apoptosis_markers().

• proliferation_key (str) – Key in obs where to store the proliferation scores.

• apoptosis_key (str) – Key in obs where to store the apoptosis scores.

• kwargs (Any) – Keyword arguments for score_genes().

Return type:

BirthDeathMixin

Returns:

: Returns self and updates the following fields:

• proliferation_key - key in obs where proliferation scores are stored.

• apoptosis_key - key in obs where apoptosis scores are stored.