readfcs.ReadFCS#
- class readfcs.ReadFCS(filepath, data_set=0)#
Bases:
object
Read in fcs file using fcsparesr as preprocess the metadata.
- Parameters:
filepath (
Union
[str
,Path
]) – str or Path location of fcs file to parsedata_set (
int
, default:0
) – int Index of retrieved data set in the fcs file.
Attributes
- data DataFrame#
Data matrix.
- header dict#
Header.
- 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