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 :
float|NoneOptional[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.
- adata :
- Returns
adata – if copy=True it returns or else add fields to adata:
- .uns[‘root_milestone->milestoneA<>milestoneB’][‘fork’][‘branch’]
assigned branch.
- Return type