make_deg_net: Prioritize ligand-receptor interactions based on differential...

In yuliangwang/talklr: Uncover Perturbed Ligand-Receptor Pairs

Description

A ligand-receptor pair is considerd when both the ligand and receptor genes are enriched in one cell type (e.g., expressed 3 fold higher in cell type A than each of the other cell types) The resulting ligand-receptor network is then compared against talklr

Usage

make_deg_net(expression_data, expressed_net, fc_thresh, pseudo_count)

Arguments

expression_data	expression matrix for ligand and receptor genes. 1st column "genes" (gene symbol, upper case); remaining columns: gene expression level
expressed_net	the output from calling make_expressed_net.R function. To ensure the input network to both algorithms are the same.
fc_thresh	fold change threshold above which a gene is considered enriched
pseudo_count	a small value added to the expression matrices to avoid dividing by 0.

Value

ligand-receptor network where both ligand and receptor genes are uniquely enriched in one cell type (i.e, marker genes for each cell type)

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