limix.stats.compute_dosage¶

limix.stats.compute_dosage(X, alt=None)[source]¶

Compute dosage from allele expectation.

Parameters

X (array_like) – Allele expectations encoded as a variants-by-samples-by-alleles matrix.
ref (array_like) – Allele reference of each locus. The allele having the minor allele frequency for the provided X is used as the reference if None. Defaults to None.

Returns

dosage – Dosage encoded as a variants-by-samples matrix.

Return type

ndarray

Example

>>> from bgen_reader import read_bgen, allele_expectation, example_files
>>> from bgen_reader import compute_dosage
>>>
>>> with example_files("example.32bits.bgen") as filepath:
...     bgen = read_bgen(filepath, verbose=False)
...     variant_idx = 2
...     e = allele_expectation(bgen, variant_idx)
...     dosage = compute_dosage(e)
...     print(dosage[:5])
[0.01550294 0.99383543 1.97933958 0.99560547 1.97879027]