sc_utils.merge_gene_info

sc_utils.merge_gene_info(adata: anndata._core.anndata.AnnData)

Merges gene information from different batches

After concatenating several datasets, the gene information dataframe adata.var can have a lot of duplicate columns from all the batches.

This function merges gene_ids, feature_types and genome information from batches, inserts them in the table and removes the batch-associated columns.

Parameters

adata – Annotated data matrix.

Example

>>> datasets = [sc.read_h5ad(path) for path in paths]
>>> adata = datasets[0].concatenate(datasets[1:], join="outer")
>>> sc_utils.merge_gene_info(adata)