Get LR and downstream pathways — get_lr_path • SpaTalk

Get LR and downstream pathways and get p value of receptor-related pathways with LR-target genes by the Fisher-exact test.

Usage

get_lr_path(
  object,
  celltype_sender,
  celltype_receiver,
  ligand,
  receptor,
  min_gene_num = 5
)

Arguments

object: SpaTalk object generated from dec_cci.
celltype_sender: Name of celltype_sender.
celltype_receiver: Name of celltype_receiver.
ligand: Name of ligand from celltype_sender.
receptor: Name of receptor from celltype_receiver.
min_gene_num: Min genes number for each pathway.

Value

A list containing two data.frame. One is LR and downstream pathways, another is the p value of receptor-related pathways with LR-target genes.