Ge.get_all_variants_table

Ge.get_all_variants_table#

missionbio.mosaic.ge.Ge.get_all_variants_table

Ge.get_all_variants_table(edit_mode: str = 'indel') → DataFrame#

Get the all_variants_table DataFrame for the given edit mode. If the data is not already cached, it will be generated.

Parameters:
edit_modestr

The type of edits to consider. Can be one of “indel”, “snv”, or “indel_snv”. Default is “indel”. If “indel_snv”, both SNV and INDEL variants are considered.

Returns:
pd.DataFrame

DataFrame containing the all variants table for the specified edit mode. Contains the following columns:

  • target: Target name

  • allele: Variant allele name

  • modifications: Description of the modifications (e.g., deletion/insertion length for INDELs or “SNV” for single nucleotide variants)

  • total_alleles: Total number of alleles genotyped across all cells

  • num_alleles: Number of mutated alleles for the variant allele across all cells

  • total_cells: Total number of cells with valid genotypes

  • num_cells: Number of cells with the variant allele

  • variant_lengths: Length of the variant (for INDELs)

  • num_wt: Number of cells with wild-type genotype

  • num_mono_alleleic: Number of cells with mono-allelic edits for this variant, i.e. heterozygous edits

  • num_bi_alleleic: Number of cells with bi-allelic edits for this variant, i.e. homozygous edits

Raises:
ValueError

If the edit_mode is not one of “indel”, “snv”, or “indel_snv”.

Ge

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