sgkit.count_call_alleles

sgkit.count_call_alleles(ds, *, call_genotype='call_genotype', merge=True)

Compute per sample allele counts from genotype calls.

Parameters:

ds Dataset

Dataset containing genotype calls.

call_genotype Hashable (default: 'call_genotype')

Input variable name holding call_genotype as defined by sgkit.variables.call_genotype_spec. Must be present in ds.

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_count_spec of allele counts with shape (variants, samples, alleles) and values corresponding to the number 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.count_call_alleles(ds)["call_allele_count"].values 
array([[[1, 1],
        [1, 1]],

       [[1, 1],
        [0, 2]],

       [[1, 1],
        [1, 1]],

       [[2, 0],
        [2, 0]]], dtype=uint8)