msmu.pp.adjust_ptm_by_protein

Estimation of PTM stoichiometry by using Global Protein Data.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData object to normalise.	required
global_mdata	MuData	MuData object which contains global protein expression.	required
modality	str	PTM modality to normalise (e.g. phospho_site, {ptm}_site).	'phospho_site'
layer	str | None	Layer to normalise. If None, the default layer (.X) will be used.	None
global_mod		Modality in global_mdata to normalise PTM site. Default is 'protein'.	required
method	Literal['ridge', 'ratio']	A method for normalisation. Options: ridge, ratio. Default is 'ridge'.	'ridge'
rescale	bool	If True, rescale the data after normalisation with median value across dataset. Default is True.	True

Returns:

Type	Description
MuData	Normalised MuData object.