ehrapy.preprocessing.regress_out¶

ehrapy.preprocessing.regress_out(adata, keys, n_jobs=None, copy=False)[source]¶

Regress out (mostly) unwanted sources of variation.

Uses simple linear regression. This is inspired by Seurat’s regressOut function in R [Satija15]. Note that this function tends to overcorrect in certain circumstances.

Parameters:

adata (AnnData) – AnnData object object containing all observations.
keys (Union[str, Sequence[str]]) – Keys for observation annotation on which to regress on.
n_jobs (Optional[int]) – Number of jobs for parallel computation. None means using scanpy._settings.ScanpyConfig.n_jobs.
copy (bool) – Determines whether a copy of adata is returned.

Return type:

Optional[AnnData]

Returns:

Depending on copy returns or updates an AnnData object with the corrected data matrix.