scFates.tl.branch_specific

scFates.tl.branch_specific(adata, root_milestone, milestones, effect=None, stf_cut=0.7, up_A=0, up_p=0.05, copy=False)

Assign genes differentially expressed between two post-bifurcation branches.

Parameters:

adata AnnData

Annotated data matrix.

root_milestone

tip defining progenitor branch.

milestones

tips defining the progenies branches.

effect Optional[float] (default: None)

minimum expression differences to call gene as differentially upregulated.

stf_cut float (default: 0.7)

fraction of projections when gene passed fdr < 0.05.

up_A float (default: 0)

minimum expression increase at derivative compared to progenitor branches to call gene as branch-specific.

up_p float (default: 0.05)

p-value of expression changes of derivative compared to progenitor branches to call gene as branch-specific.

copy bool (default: False)

Return a copy instead of writing to adata.

Returns:

adata : anndata.AnnData if copy=True it returns or else add fields to adata:

.uns[‘root_milestone->milestoneA<>milestoneB’][‘fork’][‘branch’]

assigned branch.