readfcs.ReadFCS

class readfcs.ReadFCS(filepath, data_set=0, ignore_offset_error=False, ignore_offset_discrepancy=False, use_header_offsets=False)

Bases: object

Read in fcs file using flowio.FlowData and preprocess the metadata.

Parameters:

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

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

• ignore_offset_error (bool, default: False) – Ignore data offset error. Default is False

• ignore_offset_discrepancy (bool, default: False) – Ignore discrepancy between the HEADER and TEXT values for the DATA byte offset location. Default is False

• use_header_offsets (bool, default: False) – Use the HEADER section for the data offset locations. Default is False. Setting this option to True also suppresses an error in cases of an offset discrepancy.

Attributes

property channels: DataFrame

Channels.

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