scvelo.inference.get_parameters¶
-
scvelo.inference.
get_parameters
(adata, use_rep, time_key, experiment_key, n_neighbors, x0, n_jobs=None)¶ Estimates parameters of splicing kinetics from metabolic labeling data.
See [Weiler et al., 2023].
- adata
AnnData object containing data.
- use_rep
Layer name containing labeled mRNA data.
- time_key
Column in
adata.obs
with labeling time of observations.- experiment_key
Column in
adata.obs
with experimt type of observations.- n_neighbors
TODO
- x0
The initial parameter estimate to use if provided.
- n_job
Number of optimization problems to solve in parallel.
- Returns
Estimated parameters alpha (transcription rate), gamma (degradation rate), r0 (initial GEX if
data from chase experiment is included), and success (flag if optimization ran successfully).