ehrapy.preprocessing.combat

ehrapy.preprocessing.combat(adata, key='batch', covariates=None, inplace=True)[source]

ComBat function for batch effect correction [Johnson07] [Leek12] [Pedersen12].

Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across features. This uses the implementation combat.py [Pedersen12].

Parameters:

  • adata (AnnData) – AnnData object object containing all observations.

  • key (str) – Key to a categorical annotation from obs that will be used for batch effect removal.

  • covariates (Optional[Collection[str]]) – Additional covariates besides the batch variable such as adjustment variables or biological condition. This parameter refers to the design matrix X in Equation 2.1 in [Johnson07] and to the mod argument in the original combat function in the sva R package. Note that not including covariates may introduce bias or lead to the removal of signal in unbalanced designs.

  • inplace (bool) – Whether to replace adata.X or to return the corrected data

Return type:

Union[AnnData, ndarray, None]

Returns:

Depending on the value of inplace, either returns the corrected matrix or modifies adata.X.