Get ligand-target signaling paths between ligand(s), receptors, and target gene(s) of interest

get_ligand_signaling_path_with_receptor Extract possible signaling paths between a ligand(s), receptor(s) and target gene(s) of interest. The most highly weighted path(s) will be extracted.

Usage

get_ligand_signaling_path_with_receptor(ligand_tf_matrix, ligands_all, receptors_all, targets_all, top_n_regulators = 3, weighted_networks, ligands_position = "cols")

Arguments

ligand_tf_matrix

A matrix of ligand-regulator probability scores

ligands_all

A character vector of one or more ligands of interest

receptors_all

A character vector of one or more receptors of interest

targets_all

A character vector of one or more target genes of interest

top_n_regulators

The number of top regulators that should be included in the ligand-target signaling network. Top regulators are regulators that score both high for being upstream of the target gene(s) and high for being downstream of the ligand. Default: 4.

weighted_networks

A list of two elements: lr_sig: a data frame/ tibble containg weighted ligand-receptor and signaling interactions (from, to, weight); and gr: a data frame/tibble containng weighted gene regulatory interactions (from, to, weight)

ligands_position

Indicate whether the ligands in the ligand-target matrix are in the rows ("rows") or columns ("cols"). Default: "cols".

Value

A list containing 2 elements (sig and gr): the integrated weighted ligand-signaling and gene regulatory networks data frame / tibble format with columns: from, to, weight

Examples

if (FALSE) { # \dontrun{
weighted_networks <- construct_weighted_networks(lr_network, sig_network, gr_network, source_weights_df)
ligands <- list("TNF", "BMP2", c("IL4", "IL13"))
ligand_tf_matrix <- construct_ligand_tf_matrix(weighted_networks, lr_network, ligands, ltf_cutoff = 0.99, algorithm = "PPR", damping_factor = 0.5, ligands_as_cols = TRUE)
all_ligands <- c("BMP2")
all_receptors <- c("BMPR2")
all_targets <- c("HEY1")
top_n_regulators <- 2
ligand_target_signaling_list <- get_ligand_signaling_path_with_receptor(ligand_tf_matrix, all_ligands, all_receptors, all_targets, top_n_regulators, weighted_networks)
} # }