`msmu._preprocessing._normalise._normalise`

adjust_ptm_by_protein

adjust_ptm_by_protein(mdata, global_mdata, ptm_mod='phospho_site', method='ridge', rescale=True)

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
`ptm_mod`	`str`	PTM modality to normalise (e.g. phospho_site, {ptm}_site).	`'phospho_site'`
`global_mod`	`str`	Modality in global_mdata to normalise PTM site. Default is 'protein'.	required
`method`	`str`	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:

Name	Type	Description
`mdata`	`MuData`	Normalised MuData object.

feature_scale(mdata, method, modality, gis_prefix=None, gis_col=None, rescale=True)

Feature scale data in MuData object.

Parameters:

Name	Type	Description	Default
`mdata`	`MuData`	MuData object to normalise.	required
`method`	`str`	Normalisation method to use. Options are 'gis', 'median_center'.	required
`modality`	`str`	Modality to normalise.	required
`gis_prefix`	`str \| None`	Prefix for GIS samples. If None, all samples with 'gis' in the name will be used.	`None`
`gis_col`	`list[str] \| None`	Column name for GIS samples. If None, all samples with 'gis' in the name will be used.	`None`
`rescale`	`bool`	If True, rescale the data after normalisation with median value across dataset. This is only applicable for median normalisation.	`True`

Returns:

Name	Type	Description
`mdata`	`MuData`	Normalised MuData object.

get_modality_dict(mdata, level=None, modality=None)

Get modality data from MuData object

normalise(mdata, method, modality, fraction=False, rescale=True)

Normalise data in MuData object.

Parameters:

Name	Type	Description	Default
`mdata`	`MuData`	MuData object to normalise.	required
`method`	`str`	Normalisation method to use. Options are 'quantile', 'median', 'total_sum (not implemented)'.	required
`modality`	`str`	Modality to normalise. If None, all modalities at the specified level will be normalised.	required
`fraction`	`bool`	If True, normalise within fractions. If False, normalise across all data. "fraction" yet supports fractionated TMT.	`False`
`rescale`	`bool`	If True, rescale the data after normalisation with median value across dataset. This is only applicable for median normalisation.	`True`

Returns:

Name	Type	Description
`mdata`	`MuData`	Normalised MuData object.