determine_drug_targets {DrDimont}

Determine drug target nodes in network

Description

Finds node IDs of network nodes in 'graphs' that are targeted by a drug in 'drug_target_interactions'. Returns list of node ids and list of adjacent edges.

Usage

determine_drug_targets(graphs, annotations, drug_target_interactions, settings)

Arguments

graphs

[list] A named list with elements 'groupA' and 'groupB' containing the combined graphs of each group as iGraph object ('graphs' from output of generate_combined_graphs)

annotations

[list] List of data frames that map node IDs to identifiers. Contains 'both' with unique identifiers across the whole data (output of generate_combined_graphs)

drug_target_interactions

[list] Named list specifying drug target interactions for drug response score computation

settings

[list] A named list containing pipeline settings. The settings list has to be initialized by drdimont_settings. Items in the named list can be adjusted as desired.

Value

A named list with elements 'targets' and 'edgelists'. 'targets' is a named list with elements 'target_nodes' and 'drugs_to_target_nodes'. 'target_nodes' is a data frame with column 'node_id' (unique node IDs in the iGraph object targeted by drugs) and columns 'groupA' and 'groupB' (bool values specifying whether the node is contained in the combined graph of the group). Element 'drugs_to_target_nodes' contains a named list mapping drug names to a vector of their target node IDs. 'edgelists' contains elements 'groupA' and 'groupB' containing each a list of edges adjacent to drug target nodes.

Examples

data(drug_gene_interactions)
data(combined_graphs_example)

example_settings <- drdimont_settings()

example_drug_target_interactions <- make_drug_target(target_molecules='protein',
                                        interaction_table=drug_gene_interactions,
                                        match_on='gene_name')

example_drug_target_edges <- determine_drug_targets(
                                 graphs=combined_graphs_example$graphs,
                                 annotations=combined_graphs_example$annotations,
                                 drug_target_interactions=example_drug_target_interactions,
                                 settings=example_settings)