determine_drug_targets: Determine drug target nodes in network

In molnet-org/molnet: Predicting Differential Drug Response using Multi-Omics Networks

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

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)

molnet-org/molnet documentation built on Dec. 21, 2021, 8:59 p.m.