scFates.pp.batch_correct#
- scFates.pp.batch_correct(adata, batch_key, layer='X', depth_scale=1000.0, device='cpu', inplace=True)#
batch correction of the count matrix.
Code has been translated from pagoda2 R function setCountMatrix (plain model).
- Parameters:
- adata
Annotated data matrix.
- batch_key
Column name to use for batch.
- layer default:
'X' Which layer to correct, if layer doesn’t exist, then correct X and save to layer
- depth_scale default:
1000.0 Depth scale.
- device default:
'cpu' Run method on either cpu or on gpu.
- copy
Return a copy instead of writing to adata.
- Returns:
adata : anndata.AnnData if inplace=False it returns the corrected matrix, else it update field to adata:
- .X
batch-corrected count matrix.