moscot.base.problems.BirthDeathProblem.estimate_marginals¶
- BirthDeathProblem.estimate_marginals(adata, source, proliferation_key=None, apoptosis_key=None, scaling=None, beta_max=1.7, beta_min=0.3, beta_center=0.25, beta_width=0.5, delta_max=1.7, delta_min=0.3, delta_center=0.1, delta_width=0.2)[source]¶
Estimate the source or target marginals based on marker genes, either with the birth-death process, as suggested in [Schiebinger et al., 2019], or with an exponential kernel.
See
score_genes_for_marginals()
on how to compute the proliferation and apoptosis scores.- Parameters:
adata (
AnnData
) – Annotated data object.source (
bool
) – Whether to estimate the source or the target marginals.proliferation_key (
Optional
[str
]) – Key inobs
where proliferation scores are stored.apoptosis_key (
Optional
[str
]) – Key inobs
where apoptosis scores are stored.scaling (
Optional
[float
]) – A parameter for prior growth rate estimation. Iffloat
is passed, it will be used as a scaling parameter in an exponential kernel with proliferation and apoptosis scores. IfNone
, parameters corresponding to the birth and death processes will be used.
- Return type:
- Returns:
: The estimated source or target marginals of shape
[n,]
or[m,]
, depending on thesource
. Ifsource = True
, also updates the following fields:prior_growth_rates
- prior estimate of the source growth rates.
Examples