infercnvpy.io.genomic_position_from_gtf#
- infercnvpy.io.genomic_position_from_gtf(gtf_file, adata=None, *, gtf_gene_id='gene_name', adata_gene_id=None, inplace=True)#
Get genomic gene positions from a GTF file.
The GTF file needs to match the genome annotation used for your single cell dataset.
Warning
Currently only tested with GENCODE GTFs.
- Parameters:
adata (
Optional
[AnnData
] (default:None
)) – Adds the genomic positions toadata.var
. If adata is None, returns a data frame with the genomic positions instead.gtf_gene_id (
Literal
['gene_id'
,'gene_name'
] (default:'gene_name'
)) – Use this GTF column to match it to anndataadata_gene_id (
Optional
[str
] (default:None
)) – Match this column to the gene ids from the GTF file. Default: use adata.var_names.inplace (
bool
(default:True
)) – If True, add the annotations directly to adata, otherwise return a dataframe.
- Return type: