LikelihoodMethod.label_cells

LikelihoodMethod.label_cells#

missionbio.demultiplex.dna.likelihood.LikelihoodMethod.label_cells

LikelihoodMethod.label_cells(dna: Optional[Assay] = None, *, af: Optional[DataFrame] = None, dp: Optional[DataFrame] = None, filter_ado: bool = True, min_fraction_genotyped: float = 0.3, min_fraction_match: float = 0.7) → ndarray#

Run the demultiplexing

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

  • filter_ado – Whether to filter cells that have more than 50% of the variants with possible ADO

  • min_fraction_genotyped – The minimum fraction of variants genotyped in a cell. The variants that are included in the computation of this fraction are the ones which are present in both the DNA and the truth data. These variants must also be genotyped in at least min_fraction_genotyped cells.

  • min_fraction_match – The minimum fraction of matches required between the truth genotype and the genotype of the cell. The mismatches are weighted. A mismatch for a HET call is weighted at 0.75, missing calls are weighted at 0.15 and all other mismatches are weighted at 1. The fraction of the sum of the weights to the number of genotyped variants is the fraction mismatched. The inverse of that is the fraction matched, which should be greater than this value. It is not recommended to have this lower than 0.65 or greater than 0.85

Returns:

The labels assigned to the cells

< Class LikelihoodMethod

Contents