`msmu._preprocessing._infer_protein`

get_protein_mapping

get_protein_mapping(peptides, proteins)

Infer protein grouping information.

Parameters:

Name	Type	Description	Default
`peptides`	`Series`	peptide information	required
`proteins`	`Series`	protein information	required

Returns:

Name	Type	Description
`peptide_map`	`DataFrame`	peptide mapping information
`protein_map`	`DataFrame`	protein mapping information
`protein_info`	`DataFrame`	protein information

infer_protein(mdata, propagated_from=None)

Infer protein grouping information and classify peptides.

Parameters:

Name	Type	Description	Default
`mdata`	`MuData`	MuData object	required
`propagated_from`	`MuData \| str \| None`	mudata which contains inference info (for PTM normalisation with global proteins). Can be path to global data .h5mu or mudata object. Default is None	`None`

Returns:

Name	Type	Description
`mdata`	`MuData`	MuData object with updated protein mappings

select_canon_prot(protein_group, protein_info)

DEPRECATED: Use select_representative instead.

Select canonical protein from protein list based on priority. canonical > swissprot > trembl > contam

Parameters:

Name	Type	Description	Default
`protein_group`	`str`	protein group (uniprot entry)	required

Returns:

Name	Type	Description
`protein_group`	`str`	canonical protein group

select_representative(protein_group, protein_info)

Select canonical protein from protein list based on priority. canonical > swissprot > trembl > contam

Parameters:

Name	Type	Description	Default
`protein_list`	`list[str]`	list of proteins (uniprot entry)	required
`protein_info`	`DataFrame`	DataFrame of protein info from mdata.uns['protein_info']	required

Returns:

Name	Type	Description
`protein_group`	`str`	canonical protein group