readfcs.read

readfcs.read(filepath, reindex=True, ignore_offset_error=False, ignore_offset_discrepancy=False, use_header_offsets=False)

Read in fcs file as AnnData.

Parameters:

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

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

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

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

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

Return type:

AnnData

Returns:

An AnnData object