snapatac2.tl.link_tf_to_gene#

snapatac2.tl.link_tf_to_gene(network)[source]#

Create a transcription-factor-to-gene network.

Use this function after add_tf_binding has added motif-to-region edges to a region-gene network. A TF is linked to a gene when its motif binds a region that is linked to that gene.

Anti-Patterns#

Do NOT call this before add_tf_binding; no motif-to-region paths will exist.
Do NOT treat the returned graph as weighted unless you add scores after conversion; new TF-gene edges contain default LinkData.

param network:: Graph containing gene, region, and motif nodes.
type network:: PyDiGraph
returns:: Directed graph containing TF gene nodes linked to target gene nodes.
rtype:: PyDiGraph

Examples

>>> import snapatac2 as snap
>>> network = snap.tl.init_network_from_annotation(["chr1:10000-10500"], snap.genome.hg38)
>>> tf_network = snap.tl.link_tf_to_gene(network)
>>> tf_network.num_edges() >= 0
True