LikelihoodMethod.assignment_logl

LikelihoodMethod.assignment_logl#

missionbio.demultiplex.dna.likelihood.LikelihoodMethod.assignment_logl

LikelihoodMethod.assignment_logl(dna: Optional[Assay] = None, *, af: Optional[DataFrame] = None, dp: Optional[DataFrame] = None, mixing_rate: float = 0.2) → DataFrame#

The loglikelihood of assigning each cell to each clone adjusted using the mixing rate

Parameters:

  • dna – DNA assay object. Either af and dp or dna must be provided.

  • af – The allele frequency of the variants. If not provided, it will be obtained from dna

  • dp – The depth of the variants. If not provided, it will be obtained from dna

  • mixing_rate – The expected rate of doublets in the data. This is used to set the prior probabilities for the samples. The prior for singlets is set to (1 - mixing_rate) and the prior for doublets is set to mixing_rate. Doublets are assumed to be labels in the truth that contain a colon (“:”).

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