Frequency

bgen_reader.allele_frequency(expec)

Compute allele frequency from its expectation.

Parameters

expec (array_like) – Allele expectations encoded as a samples-by-alleles matrix.

Returns

Allele frequencies encoded as a variants-by-alleles matrix.

Return type

numpy.ndarray

Examples

>>> from bgen_reader import read_bgen, example_filepath
>>> from bgen_reader import allele_expectation, allele_frequency
>>>
>>> filepath = example_filepath("example.32bits.bgen")
>>>
>>> bgen = read_bgen(filepath, verbose=False)
>>>
>>> variants = bgen["variants"]
>>> samples = bgen["samples"]
>>> genotype = bgen["genotype"]
>>>
>>> variant = variants[variants["rsid"] == "RSID_6"].compute()
>>> variant_idx = variant.index.values[0]
>>>
>>> p = genotype[variant_idx].compute()["probs"]
>>> # For unphased genotypes only.
>>> e = allele_expectation(bgen, variant_idx)
>>> f = allele_frequency(e)
>>>
>>> alleles = variant["allele_ids"].values[0].split(",")
>>> print(alleles[0] + ": {}".format(f[0]))
A: 229.23103218810434
>>> print(alleles[1] + ": {}".format(f[1]))
G: 270.7689678118956
>>> print(variant)
        id    rsid chrom   pos  nalleles allele_ids  vaddr
4  SNPID_6  RSID_6    01  6000         2        A,G  19377