LR_pathway: Construction of intracellular signaling pathway

In Jasonxu0109/PlantPhoneDB: PlantPhoneDB in R

Construction of intracellular signaling pathway

Description

Construction of intracellular signaling pathway

Usage

LR_pathway(lr, objs, CellA, CellB, neighbor, geneSet, cor_value = 0.013, ...)

Arguments

lr	A data frame of the ligand-receptor interactions.
objs	object Seurat object.
CellA	Ligands cell.
CellB	Receptors cell.
neighbor	Represents the second-order neighbors of ligand-receptor pair in the signaling network.Default is 2.
geneSet	KEGG gene sets. (Ma et al., Nucleic Acids Research, 2021).
cor_value	Spearman’s correlation between mean expression of ligand-receptor pair and expression of each downstream gene. Default is 0.013.
...

Value

A data frame of the significantly enriched gene sets for each gene set category.

Jasonxu0109/PlantPhoneDB documentation built on Jan. 2, 2023, 8:53 p.m.