scvelo.tl.differential_kinetic_test

scvelo.tl.differential_kinetic_test(data, var_names='velocity_genes', groupby=None, use_raw=None, return_model=None, add_key='fit', copy=None, **kwargs)

Test to detect cell types / lineages with different kinetics.

Likelihood ratio test for differential kinetics to detect clusters/lineages that display kinetic behavior that cannot be sufficiently explained by a single model for the overall dynamics. Each cell type is tested whether an independent fit yields a significantly improved likelihood.

data: AnnData

Annotated data matrix.

var_names: str, list of str (default: ‘velocity_genes)

Names of variables/genes to use for the fitting.

groupby: str (default: None)

Key of observations grouping to consider, e.g. ‘clusters’.

use_raw: bool (default: False)

Whether to use raw data for estimation.

add_key: str (default: ‘fit’)

Key to add to parameter names, e.g. ‘fit_t’ for fitted time.

copy: bool (default: None)

Return a copy instead of writing to adata.

Returns

• fit_pvals_kinetics (.varm) – P-values of competing kinetic for each group and gene

• fit_diff_kinetics (.var) – Groups that have differential kinetics for each gene.