cellink.utils.one_hot_encode_genotypes

cellink.utils.one_hot_encode_genotypes(adata)

Convert genotypes to one-hot encoding.

This function takes the genotype data in adata and converts it into a one-hot encoded format. Each genotype (e.g., homozygous reference, heterozygous, homozygous alternate) is transformed into a binary vector representation.

Params

adata

The annotated data matrix of shape n_obs x n_vars. Rows correspond to individuals and columns to variants.

rtype:

AnnData | ndarray | None

returns:

Returns the one-hot encoded genotypes or updates adata with the new representation, depending on inplace.

Example

>>> import numpy as np
>>> from anndata import AnnData
>>> adata = AnnData(
...     np.array(
...         [
...             [0, 1, 2],
...             [1, 0, 1],
...             [2, 2, 0],
...         ]
...     )
... )
>>> one_hot_encoded = one_hot_encode_genotypes(adata, key_added="one_hot", inplace=False)
>>> one_hot_encoded
array([[[1, 0, 0],
        [0, 1, 0],
        [0, 0, 1]],

[[0, 1, 0],

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

[[0, 0, 1],

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