msmu.pp.normalise

Normalise data in MuData object.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData object to normalise.	required
method	NormalisationMethod	Normalisation method to use. Options are 'quantile', 'median', 'total_sum'.	required
modality	str	Modality to normalise.	required
layer	str | None	Layer to normalise. If None, the default layer (.X) will be used.	None
group_obs	str | None	Column name in adata.obs defining sample groups. If provided, normalisation is performed independently within each group. If None, no obs grouping is applied.	None
group_var	str | None	Column name in adata.var defining feature groups (e.g. "filename" for fractionated TMT or label-free workflows). If provided, normalisation is performed independently within each group. If None, no var grouping is applied.	None
batch_key	str | None	Deprecated alias for group_obs.	None
fraction_key	str | None	Deprecated alias for group_var.	None
fraction	bool	Deprecated. If True, equivalent to group_var="filename".	False

Returns:

Type	Description
MuData	Normalised MuData object.

Notes

When both group_obs and group_var are provided, normalisation is performed independently within each (obs-group × var-group) block.