peach.pp.compute_pathway_scores#
- peach.pp.compute_pathway_scores(adata, net=None, use_layer=None, obsm_key='pathway_scores', verbose=True)[source]#
Compute pathway activity scores using MSigDB pathways.
- Parameters:
adata (AnnData) – Annotated data object
net (pd.DataFrame, optional) – Pathway network dataframe. If None, will load using sources parameter
use_layer (str, optional) – Layer in adata to use for scoring
obsm_key (str, default: "pathway_scores") – Key in adata.obsm to store pathway scores
verbose (bool, default: True) – Whether to print progress
- Return type: