COMPASS.run

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COMPASS.run#

missionbio.mosaic.algorithms.compass.COMPASS.run

COMPASS.run(kwargs=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:
kwargsdict

Passed to COMPASS. Example {”–chains”: “5”}

< Class COMPASS

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