scirpy.io.read_tracer

scirpy.io.read_tracer(path)

Read data from TraCeR ([SLonnbergP+16]).

Requires the TraCeR output directory which contains a folder for each cell. Unfortunately the results files generated by tracer summarize do not contain all required information.

The function will read TCR information from the filtered_TCR_seqs/<CELL_ID>.pkl files.

Currently, reading data into Scirpy has the following limitations:

  • only alpha- and beta TCR chains are supported. Other chains are ignored.

  • non-productive chains are removed

  • Each chain can contain up to two alpha and two beta chains (Dual TCR). Excess chains are removed (those with lowest read count/UMI count) and cells flagged as Multichain-cell.

For more information, see T-cell receptor model.

Parameters
path : str, PathUnion[str, Path]

Path to the TraCeR output folder.

Return type

AnnDataAnnData

Returns

AnnData object with TCR data in obs for each cell. For more details see Data structure.