limix.qc.compute_maf¶

limix.qc.compute_maf(X)[source]¶

Compute minor allele frequencies.

It assumes that X encodes 0, 1, and 2 representing the number of alleles (or dosage), or NaN to represent missing values.

Parameters:	X (array_like) – Genotype matrix.
Returns:	Minor allele frequencies.
Return type:	array_like

Examples

>>> from numpy.random import RandomState
>>> from limix.qc import compute_maf
>>>
>>> random = RandomState(0)
>>> X = random.randint(0, 3, size=(100, 10))
>>>
>>> print(compute_maf(X)) 
[0.49  0.49  0.445 0.495 0.5   0.45  0.48  0.48  0.47  0.435]