- scanpy.pp.combat(adata, key='batch', covariates=None, inplace=True)
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 genes. This uses the implementation combat.py [Pedersen12].
- adata :
Annotated data matrix
- key :
Key to a categorical annotation from
obsthat will be used for batch effect removal.
- covariates :
Additional covariates besides the batch variable such as adjustment variables or biological condition. This parameter refers to the design matrix
Xin Equation 2.1 in [Johnson07] and to the
modargument in the original combat function in the sva R package. Note that not including covariates may introduce bias or lead to the removal of biological signal in unbalanced designs.
- inplace :
Whether to replace adata.X or to return the corrected data
- adata :
- Return type:
: Depending on the value of
inplace, either returns the corrected matrix or or modifies