create_pseudobulk

hnoca.stats.pseudobulk.create_pseudobulk(adata, sample_key='batch', group_key=None, layer=None, mode='sum', min_cells=10, min_counts=1000, **kwargs)

Create pseudobulk data from anndata object

Parameters:

Name	Type	Description	Default
adata	AnnData	AnnData object	required
sample_key	str	Column name in adata.obs that contains the sample ID	'batch'
group_key	Optional[str]	Column name in adata.obs that contains the group ID	None
layer	Optional[str]	Layer to use for pseudobulk data. If None, use adata.X	None
mode	str	Method to aggregate data. Default is 'sum'.	'sum'
min_cells	int	Filter to remove samples by a minimum number of cells in a sample-group pair.	10
min_counts	int	Filter to remove samples by a minimum number of summed counts in a sample-group pair.	1000
**kwargs		Additional arguments to pass to decoupler.get_pseudobulk()	{}

Returns:

Type	Description
AnnData	AnnData object with pseudobulk data