sgkit.call_allele_frequencies

sgkit.call_allele_frequencies(ds, *, call_allele_count='call_allele_count', merge=True)

Compute per sample allele frequencies from genotype calls.

Parameters:

ds Dataset

Dataset containing genotype calls.

call_allele_count Hashable (default: 'call_allele_count')

Input variable name holding call_allele_count as defined by sgkit.variables.call_allele_count_spec. If the variable is not present in ds, it will be computed using count_call_alleles().

merge bool (default: True)

If True (the default), merge the input dataset and the computed output variables into a single dataset, otherwise return only the computed output variables. See Dataset merge behavior for more details.

Return type:

Dataset

Returns:

: A dataset containing sgkit.variables.call_allele_frequency_spec of allele frequencies with shape (variants, samples, alleles) and values corresponding to the frequency of non-missing occurrences of each allele.

Examples

>>> import sgkit as sg
>>> ds = sg.simulate_genotype_call_dataset(n_variant=4, n_sample=2, seed=1)
>>> sg.display_genotypes(ds) 
samples    S0   S1
variants
0         1/0  1/0
1         1/0  1/1
2         0/1  1/0
3         0/0  0/0
>>> sg.call_allele_frequencies(ds)["call_allele_frequency"].values 
array([[[0.5, 0.5],
        [0.5, 0.5]],

       [[0.5, 0.5],
        [0. , 1. ]],

       [[0.5, 0.5],
        [0.5, 0.5]],

       [[1. , 0. ],
        [1. , 0. ]]])