get_target_genes_ligand_oi: Get a set of predicted target genes of a ligand of interest

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

Get a set of predicted target genes of a ligand of interest

Description

get_target_genes_ligand_oi Get a set of predicted target genes of a ligand of interest.

Usage

get_target_genes_ligand_oi(ligand_oi, ligand_target_matrix, error_rate = 0.1, cutoff_method = "distribution", fdr_method = "global", output = "logical",ligands_position = "cols")

Arguments

ligand_oi	The ligand of interest of which top target genes should be returned
ligand_target_matrix	A matrix of ligand-target probabilty scores.
error_rate	FDR for cutoff_method "fdrtool" and "distribution"; number between 0 and 1 indicating which top fraction of target genes should be returned for cutoff_method "quantile". Default: 0.1
cutoff_method	Method to determine which genes can be considered as a target of a ligand and which genes not, based on the ligand-target probability scores. Possible options: "distribution", "fdrtool" and "quantile". Default: "distribution".
fdr_method	Only relevant when cutoff_method is "fdrtool". Possible options: "global" and "local". Default: "global".
output	Determines whether a vector with target gene names should be returned ("gene_symbols") or a logical vector indicating for every target gene whether or not it is a target ("logical").
ligands_position	Indicate whether the ligands in the ligand-target matrix are in the rows ("rows") or columns ("cols"). Default: "cols"

Value

A vector with target gene names should be returned ("gene_symbols") or a logical vector indicating for every target gene whether or not it is a target ("logical").

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 = get_target_genes_ligand_oi("BMP2", ligand_target_matrix, error_rate = 0.1, cutoff_method = "distribution", fdr_method = "global", output = "logical",ligands_position = "cols")

## End(Not run)

saeyslab/nichenetr documentation built on Sept. 7, 2024, 10:27 a.m.