make_expressed_net_specify_expressed_genes: Prioritize ligand-receptor interactions in a single condition

In yuliangwang/talklr: Uncover Perturbed Ligand-Receptor Pairs

Description

Instead of using an expression threshold, this function identifies interesting ligand-receptor pairs among a specific list of expressed genes provided by the user. Run this function separately for perturbed and baseline conditions before running disease_vs_normal_KL.R, so that ligand and receptor matrices are in the same order.

Usage

make_expressed_net_specify_expressed_genes(
  expression_data,
  expressed_genes,
  receptor_ligand,
  KL_method
)

Arguments

expression_data	expression matrix for ligand and receptor genes. 1st column "genes" (gene symbol, upper case); remaining columns: gene expression level
expressed_genes	a character vector of expressed genes
receptor_ligand	receptor-ligand interaction database from Ramilowski JA et al, Nat. Comm. 2015. Provided with the package
KL_method	"product" or "min": ligand-receptor interaction score is either defined by multiplying ligand and receptor expression values or take the minimum

Value

KL divergence for all expressed ligand-receptor pairs, as well as ligand and receptor expression values across cell types. You may want to sort from highest to lowest to examine the top ones.

yuliangwang/talklr documentation built on Feb. 17, 2020, 5:02 a.m.