extract_top_n_targets: Get the predicted top n target genes of a ligand of interest

In browaeysrobin/nichenetr: Modeling Intercellular Communication by Linking Ligands to Target Genes with NicheNet

Get the predicted top n target genes of a ligand of interest

Description

extract_top_n_targets Get the predicted top n target genes of a ligand of interest.

Usage

extract_top_n_targets(ligand_oi,top_n,ligand_target_matrix,ligands_position = "cols")

Arguments

ligand_oi	The ligand of interest of which top target genes should be returned
top_n	A number between 0 and the total nr of target genes indicating which top n of target genes should be returned.
ligand_target_matrix	A matrix of ligand-target probabilty scores.
ligands_position	Indicate whether the ligands in the ligand-target matrix are in the rows ("rows") or columns ("cols"). Default: "cols"

Value

A named numeric vector of ligand-target gene probability scores of the top target genes.

Examples

## Not run: 
## Generate the ligand-target matrix from loaded weighted_networks
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2",c("IL4","IL13"))
ligand_target_matrix = construct_ligand_target_matrix(weighted_networks, ligands)
targets = extract_top_n_targets("BMP2",50,ligand_target_matrix)

## End(Not run)

browaeysrobin/nichenetr documentation built on Sept. 9, 2024, 11:25 a.m.