scanpy.pp.combat

scanpy.pp.combat(adata, key='batch', inplace=True)

ComBat function for batch effect correction [Johnson07] [Leek12] [Pedersen12].

Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat [Pedersen12].

Parameters:
adata : AnnData

Annotated data matrix

key : str, optional (default: "batch")

Key to a categorical annotation from adata.obs that will be used for batch effect removal

inplace : bool, optional (default: True)

Wether to replace adata.X or to return the corrected data

Returns:

or modifies the passed one.

Return type:

Depending on the value of inplace, either returns an updated AnnData object