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Determine expressed ligands of a list of cell types

get_expressed_ligands.Rd

Identifies ligands (as classified in lr_network) that are expressed above proportion_cutoff fraction of cells in each cellt ype.

Usage

get_expressed_ligands(
  obj,
  sender_cluster_key,
  sender_cluster_names,
  proportion_cutoff = 0.01,
  lr_network
)

Arguments

obj

Seurat object containing niche cell data

sender_cluster_key

column name in sender_obj@meta.data that denotes the clusters.

sender_cluster_names

Clusters in sender_cluster_key to use.

proportion_cutoff

Pct cutoff to threshold a ligand as active. A ligand is 'active' if it is expressed in more than proportion_cutoff fraction of cells in the sender cluster.

lr_network

NicheNet ligand-receptor pairs data file.

Value

A character vector with the gene symbols of the expressed ligands