arcfish.wr.caller_wrapper#

arcfish.wr.caller_wrapper(loader: FOF_CT_Loader, loop: LoopCaller | None = None, loop_path: Path | None = None, tad: TADCaller | None = None, tad_path: Path | None = None, cpmt: ABCaller | None = None, cpmt_path: Path | None = None)#

Call loops/TADs/compartments for all chromosomes.

Call chromatin loops, TADs, or A/B compartments from all chromosomes in the dataset. Create and process adata object and pass it to all callers passed in to avoid re-computing the pairwise difference.

Can pass in any combinations of loops, TADs, and compartments by specifying the calling object and the path.

Parameters:

  • loader (pp.FOF_CT_Loader) – Data loader with data paths.

  • loop (tl.LoopCaller | None, optional) – Instantiated loop caller object, by default None.

  • loop_path (Path | None, optional) – File to store loop calling result, by default None.

  • tad (tl.TADCaller | None, optional) – Instantiated TAD caller object, by default None.

  • tad_path (Path | None, optional) – File to store TAD calling result, by default None.

  • cpmt (tl.ABCaller | None, optional) – Instantiated A/B compartment object, by default None.

  • cpmt_path (Path | None, optional) – File to store A/B compartment calling result, by default None.

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