readfcs.ReadFCS

class readfcs.ReadFCS(filepath, data_set=0)

Bases: object

Read in fcs file using fcsparesr as preprocess the metadata.

Parameters:

• filepath (str | Path) – str or Path location of fcs file to parse

• data_set (int, default: 0) – int Index of retrieved data set in the fcs file.

Attributes

property data: DataFrame

Data matrix.

property header: dict

Header.

property meta: dict

Metadata.

Methods

compensate()

Apply compensation to event data.

Return type:

None

to_anndata(reindex=True)

Convert the FCSFile instance to an AnnData.

Parameters:

reindex (default: True) – variables will be reindexed with marker names if possible otherwise channels

Return type:

AnnData

Returns:

an AnnData object