snapatac2.tl.init_network_from_annotation#
- snapatac2.tl.init_network_from_annotation(regions, anno_file, upstream=250000, downstream=250000, id_type='gene_name', coding_gene_only=True)[source]#
Build CRE-gene network from gene annotations.
Link CREs to genes if they are close to genes’ promoter regions.
- Parameters:
regions (
list[str]) – A list of peaks/regions, e.g.,["chr1:100-1000", "chr2:55-222"].anno_file (
Path|Genome) – The GFF file containing the transcript level annotations.upstream (
int) – Upstream extension to the transcription start site.downstream (
int) – Downstream extension to the transcription start site.id_type (
Literal['gene_name','gene_id','transcript_id']) – “gene_name”, “gene_id” or “transcript_id”.coding_gene_only (
bool) – Retain only coding genes in the network.
- Returns:
A network where peaks/regions point towards genes if they are within genes’ regulatory domains.
- Return type:
rx.PyDiGraph