COMPASS.run

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COMPASS.run#

missionbio.mosaic.algorithms.compass.COMPASS.run

COMPASS.run(path: Optional[Union[str, Path]] = None, prefix: Optional[str] = None, cnv: Optional[str] = 'LOH', kwargs: Optional[Any] = None) → None#

Process the sample using COMPASS.

By default, the CNV clone identification is disabled (–CNV 0). Only the somatic_variants are used. The germline variants are not passed to COMPASS.

The output is stored in the attributes that end with “_”

  1. nodes_ : _cellAssignments.tsv as a pd.DataFrame

  2. probability_ : _cellAssignmentProbs.tsv as a pd.DataFrame

  3. tree_ : _tree.json as a dict

  4. node_genotypes_ : _nodes_genotypes.tsv as a pd.DataFrame

  5. labels_ : The labels for the cells

Parameters:
path: str

The directory in which the input and output should be stored

prefix: str

The prefix to use for the input and output files

cnvstr

The type of CNV to call using COMPASS. Possible values are None, “LOH” and “CNV”.

kwargsdict

Passed to COMPASS. Example {”–chains”: “5”}. The –CNA command should be set using the cnv parameter.

< Class COMPASS

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