nichenetr (version 0.1.0)

get_weighted_ligand_target_links: Infer weighted active ligand-target links between a possible ligand and target genes of interest

Description

get_weighted_ligand_target_links Infer active ligand target links between possible lignands and genes belonging to a gene set of interest: consider the intersect between the top n targets of a ligand and the gene set.

Usage

get_weighted_ligand_target_links(ligand, geneset,ligand_target_matrix,n = 250)

Arguments

ligand

Character vector giving the gene symbols of the potentially active ligand for which you want to find target genes.

geneset

Character vector of the gene symbols of genes of which the expression is potentially affected by ligands from the interacting cell.

ligand_target_matrix

The NicheNet ligand-target matrix denoting regulatory potential scores between ligands and targets (ligands in columns).

n

The top n of targets per ligand that will be considered. Default: 250.

Value

A tibble with columns ligand, target and weight (i.e. regulatory potential score).

Examples

# NOT RUN {
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2","IL4")
ligand_target_matrix = construct_ligand_target_matrix(weighted_networks, ligands, ltf_cutoff = 0, algorithm = "PPR", damping_factor = 0.5, secondary_targets = FALSE)
potential_ligand = "TNF"
geneset = c("SOCS2","SOCS3", "IRF1")
active_ligand_target_links_df = get_weighted_ligand_target_links(ligand = potential_ligand, geneset = geneset, ligand_target_matrix = ligand_target_matrix, n = 250)
# }
# NOT RUN {
# }