msmu.pp.correct_batch_effect

Batch correction methods for MuData object. GIS-based normalization, median centering, ComBat, and continuous batch correction (with lowess) are supported.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData object to batch correct.	required
method	Literal['gis', 'median_center', 'combat', 'continuous']	Batch correction method to use. Options are 'gis', 'median_center', 'combat', 'continuous'.	required
category	str	Category in .obs to use for batch correction.	required
modality	str	Modality to batch correct.	required
layer	str | None	Layer to batch correct. If None, the default layer (.X) will be used.	None
gis_samples	list[str] | None	List of GIS samples.	None
drop_gis	bool	If True, GIS samples will be dropped after correction. Default is True.	True
rescale	bool	If True, rescale the data after batch correction with median value across dataset (except combat).	True
log_transformed	bool	If True, data is assumed to be log-transformed. Default is True.	True

Returns:

Type	Description
MuData	Batch corrected MuData object.