omicverse.utils.get_gene_annotation

omicverse.utils.get_gene_annotation(adata, var_by=None, gtf=None, gtf_by=None, by_func=None)[source]

Annotate adata.var by merging with gene-level GTF attributes.

Parameters:

  • adata (Input dataset.)

  • var_by (Specify a column in adata.var used to merge with GTF attributes,) – otherwise adata.var_names is used by default.

  • gtf (Path to the GTF file.)

  • gtf_by (Specify a field in the GTF attributes used to merge with adata.var,) – e.g. “gene_id”, “gene_name”.

  • by_func (Specify an element-wise function used to transform merging fields,) – e.g. removing suffix in gene IDs.

Return type:

None

Note

The genomic locations are converted to 0-based as specified in bed format rather than 1-based as specified in GTF format.