msmu.io.add_quant

Attach FlashLFQ peptide quantification to MuData.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData with sample metadata in .obs; may already contain a peptide modality.	required
quant_data	str | PathLike[str] | DataFrame	Tab-separated file path/URL or DataFrame with Sequence and Intensity_<sample> columns.	required
quant_tool	str	Only "flashlfq" is supported.	required
index_name	str | None	Column in global .obs used to match intensity sample names; None uses the observation index. MS filename extensions are stripped from these names.	None

Returns:

Type	Description
MuData	MuData with updated peptide.X, or a newly attached peptide modality. Existing peptide quantification is replaced in place; reassign the return value in either case.

Notes

All input samples must have intensity columns. Zeros become NaN and values are stored as float32. For an existing peptide modality, its feature/sample axes and annotations are preserved: unmatched identified peptides receive NaN and extra quantified peptides are discarded. Use mdata.copy() to preserve the original. See write_flashlfq_input to prepare FlashLFQ input.

Examples:

import msmu as mm
mdata = mm.io.add_quant(mdata, "QuantifiedPeptides.tsv", quant_tool="flashlfq")