scvi.data.organize_multiome_anndatas#
- scvi.data.organize_multiome_anndatas(multi_anndata, rna_anndata=None, atac_anndata=None, modality_key='modality')[source]#
Concatenate multiome and single-modality input anndata objects.
These anndata objects should already have been preprocessed so that both single-modality objects use a subset of the features used in the multiome object. The feature names (index of
.var
) should match between the objects.- Parameters:
multi_anndata (AnnData) – AnnData object with Multiome data (Gene Expression and Chromatin Accessibility)
rna_anndata (Optional[AnnData]) – AnnData object with gene expression data
atac_anndata (Optional[AnnData]) – AnnData object with chromatin accessibility data
modality_key (str) – The key to add to the resulting AnnData
.obs
, indicating the modality each cell originated from. Default is “modality”.
- Return type:
Notes
Features that exist in either rna_anndata or atac_anndata but do not exist in multi_anndata will be discarded.