msmu.read_fragpipe
Reads FragPipe output and returns a MuData object.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
identification_file
|
str | Path | list
|
Path to the FragPipe PSM output file(s). |
required |
label
|
Literal['tmt', 'label_free']
|
Label type ('tmt' or 'label_free'). |
required |
acquisition
|
Literal['dda', 'dia']
|
Acquisition method ('dda' or 'dia'). Note: 'dia' is not yet implemented. |
required |
quantification_file
|
str | Path | list | None
|
Path to the FragPipe quantification file(s). Required for LFQ. |
None
|
sdrf_file
|
str | Path | None
|
Optional SDRF metadata file to merge into obs. |
None
|
validate_sdrf
|
bool
|
Validate the SDRF with sdrf-pipelines if installed. Default is True. |
True
|
Returns:
| Type | Description |
|---|---|
MuData
|
A MuData object containing the FragPipe data. |