msmu.pp.to_ptm

Summarise peptide-level data to PTM-level data.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData object containing peptide-level data.	required
modi_name	str	Name of the PTM to summarise (e.g., "phospho"). Will be used in the output modality name (eg. phospho_site).	required
modification	str	Modification string (e.g., "[+79.96633]", "(unimod:21)").	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 group and "directlfq" applies the DirectLFQ rollup per group; both assume the quantification is in log2 space (apply log2_transform first).	'median'
top_n	int | None	Number of top features to consider for summarisation. If None, all features 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'

Returns:

Name	Type	Description
MuData	MuData	MuData object containing PTM-level data.