dandelion.base.tools.pseudobulk_gex

dandelion.base.tools.pseudobulk_gex(adata_raw, pbs=None, obs_to_bulk=None, obs_to_take=None)[source]

Function to pseudobulk gene expression (raw count).

Parameters:

  • adata_raw (AnnData) – Needs to have raw counts in .X

  • pbs (np.ndarray | sp.sparse.csr_matrix | None, optional) – Optional binary matrix with cells as rows and pseudobulk groups as columns

  • obs_to_bulk (list[str] | str | None, optional) – Optional obs column(s) to group pseudobulks into; if multiple are provided, they will be combined

  • obs_to_take (list[str] | str | None, optional) – Optional obs column(s) to identify the most common value of for each pseudobulk

Returns:

pb_adata whereby each observation is a cell neighbourhood

pseudobulked gene expression stored in pb_adata.X

genes stored in pb_adata.var

pseudobulk metadata stored in pb_adata.obs

pseudobulk assignment (binary matrix with input cells as columns) stored in pb_adata.obsm[‘pbs’]

Return type:

AnnData