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.
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.
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.