find_lr_path: Find lrpairs and pathways

In ZJUFanLab/SpaTalk: Infer Cell-Cell Communication for Spatial Transcriptomics

Find lrpairs and pathways

Description

Find lrpairs and pathways with receptors having downstream targets and transcriptional factors.

Usage

find_lr_path(
  object,
  lrpairs,
  pathways,
  max_hop = NULL,
  if_doParallel = T,
  use_n_cores = NULL
)

Arguments

object	SpaTalk object generated from dec_celltype.
lrpairs	A data.frame of the system data containing ligand-receptor pairs of 'Human' and 'Mouse' from CellTalkDB.
pathways	A data.frame of the system data containing gene-gene interactions and pathways from KEGG and Reactome as well as the information of transcriptional factors.
max_hop	Max hop from the receptor to the downstream target transcriptional factor to find for receiving cells. Default is 3 for human and 4 for mouse.
if_doParallel	Use doParallel. Default is TRUE.
use_n_cores	Number of CPU cores to use. Default is all cores - 2.

Value

SpaTalk object containing the filtered lrpairs and pathways.

ZJUFanLab/SpaTalk documentation built on Jan. 21, 2025, 3:13 p.m.