molnet (version 0.1.0)

determine_drug_targets: Determine drug target nodes in network

Description

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

Usage

determine_drug_targets(graphs, annotations, drug_target_interaction, settings)

Arguments

graphs

A named list with elements `group1` and `group2` containing the combined graphs of each group as iGraph object.

annotations

List of data frames that map node IDs to identifiers. Contains `all` (unique identifiers across the whole data) and `group1` and `group2` containing identifiers specific to the strata.

drug_target_interaction

Named list specifying drug target interactions for drug response score computation

settings

A named list containing pipeline settings

Value

A named list with elements `drug_targets` and `drug_target_edge_list`. * `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 `group1` and `group2` (boolean 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. * `drug_target_edge_list` contains elements `group1` and `group2` containing each a list of edges adjacent to drug target nodes.

Examples

# NOT RUN {
data(drug_gene_interactions)
data(combined_graphs_example)
combined_graphs <- combined_graphs_example
settings <- molnet_settings()
drug_target_interaction <- make_drug_target(target_molecules='protein',
interaction_table=drug_gene_interactions,
match_on='gene_name')
drug_targets <- determine_drug_targets(combined_graphs[["graphs"]],
combined_graphs[["annotations"]],
drug_target_interaction,
settings)

# }