msmu.pp.to_protein

Summarize peptide-level data to protein-level data. By default, uses every unique peptide (_shared_peptide = "discard") per protein_group for quantification aggregation with median; top_n with rank_method restricts the rollup to the top-ranked peptides.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData object containing Peptide-level data.	required
layer	str | None	Layer to use for quantification aggregation. If None, the default layer (.X) will be used. Defaults to None.	None
agg_method	Literal['median', 'mean', 'sum', 'median_polish', 'directlfq']	Aggregation method to use. One of "median", "mean", "sum", "median_polish", or "directlfq". Defaults to "median". "median_polish" applies Tukey's median polish per protein group and "directlfq" applies the DirectLFQ rollup per protein group; both assume the quantification is in log2 space (apply log2_transform first).	'median'
top_n	int | None	Number of top peptides to consider for summarization. If None, all peptides are used. Defaults to None.	None
rank_method	Literal['median_intensity', 'total_intensity', 'max_intensity', 'mean_intensity']	Method to rank features when selecting top_n. Defaults to "median_intensity".	'median_intensity'
calculate_q	bool	Whether to calculate q-values. Defaults to True.	True
_shared_peptide	Literal['discard']	How to handle shared peptides. Currently only "discard" is implemented. Defaults to "discard".	'discard'

Returns:

Type	Description
MuData	MuData object containing protein-level data.