cellink.utils.dosage_per_strand

cellink.utils.dosage_per_strand(adata)

Convert dosage to per-strand encoding.

This function takes the dosage data in adata and converts it into a per-strand encoding format. If the dosage is 0, 1, or 2, it returns standard one-hot encoding. For other dosages, it returns the relative proportion of the dosage.

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 per-strand 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, 1, 2],
...             [3, 4, 0],
...         ]
...     )
... )
>>> per_strand_encoded = dosage_per_strand(adata, key_added="dosage", inplace=False)
>>> per_strand_encoded
array([[[1. , 0. ],
        [0.5, 0.5],
        [1. , 0. ]],

[[0.5, 0.5],

[0.5, 0.5], [1. , 0. ]],

[[0.75, 0.25],

[0.8, 0.2], [0. , 1. ]]])