ehrapy.preprocessing.sqrt_norm¶

ehrapy.preprocessing.sqrt_norm(adata, vars=None, copy=False)[source]¶

Apply square root normalization.

Take the square root of all values.

Parameters:

adata (AnnData) – AnnData object containing X to normalize values in. Must already be encoded using encode().
vars (str | Sequence[str] | None) – List of the names of the numeric variables to normalize. If None all numeric variables will be normalized. Defaults to None.
copy (bool) – Whether to return a copy or act in place. Defaults to False.

Return type:

AnnData | None

Returns:

AnnData object with normalized X. Also stores a record of applied normalizations as a dictionary in adata.uns[“normalization”].

Examples

>>> import ehrapy as ep
>>> adata = ep.dt.mimic_2(encoded=True)
>>> adata_norm = ep.pp.sqrt_norm(adata, copy=True)