cpa.CPA.setup_anndata#
- classmethod CPA.setup_anndata(adata, perturbation_key, control_group, dosage_key=None, batch_key=None, layer=None, smiles_key=None, is_count_data=True, categorical_covariate_keys=[], deg_uns_key=None, deg_uns_cat_key=None, max_comb_len=2, **kwargs)[source]#
Annotation Data setup function
- Parameters:
- adata anndata.AnnData
AnnData object
- perturbation_key str
Key in adata.obs containing perturbations
- control_group str
Control group name
- dosage_key str, optional
Key in adata.obs containing perturbation dosages, by default None. If None, all dosages are set to 1.0
- batch_key str, optional
Key in adata.obs containing batch information, by default None
- layer str, optional
Key in adata.layers containing gene expression data, by default None. If None, adata.X is used
- is_count_data bool, optional
Whether the data is count data, by default False
- categorical_covariate_keys List[str], optional
List of keys in adata.obs containing categorical covariates, by default None
- deg_uns_key str, optional
Key in adata.uns containing differentially expressed genes for each combination of covariates and perturbations, by default None
- deg_uns_cat_key str, optional
Key in adata.obs containing covariate combinations for each cell, by default None
- max_comb_len int, optional
Maximum number of perturbations in a combination, by default 2