bpcells.experimental.build_cell_groups#

bpcells.experimental.build_cell_groups(fragments: str, cell_ids: Sequence[str], group_ids: Sequence[str], group_order: Sequence[str]) → ndarray[source]#

Build cell_groups array for use in pseudobulk_insertion_counts()

Parameters:

fragments (str) – Path to BPCells fragments directory
cell_ids (list[str]) – List of cell IDs
group_ids (list[str]) – List of pseudobulk IDs for each cell (same length as cell_ids)
group_order (list[str]) – Output order of pseudobulks (Contain the unique group_ids)

Returns:

Numpy array suitable as input for cell_groups in pseudobulk_insertion_counts(). Same length as total number of cells in the fragments input, specifying the output pseudobulk index for each cell (or -1 if the cell is excluded from consideration)

Return type:

numpy.ndarray