find_targets function

[INTERNAL] Filter drug target nodes

[INTERNAL] Based on the supplied target molecules, interaction table, graph and annotation this function returns a data frame containing nodes in the network targeted by a drug and a list containing the drug names as names and a vector of node IDs as keys.

find_targets(graphs, target_molecules, interaction_table, annotation, on)

Arguments

• graphs: [list] List of two iGraph graph objects (one for each group)
• target_molecules: [string] Identifies the type of the target molecules (e.g., protein). The string must be contained in the type column of the annotation data frame.
• interaction_table: [data.frame] Specifying the interaction of drugs and target molecules. Must contain a column drug_name containing drug names/identifiers and a column named like the character string given in the on argument, which must be an identifier for the targeted molecule.
• annotation: [data.frame] Contains the annotation for all the nodes contained in the combined network. Must contain a column node_id (vertex IDs in iGraph graph object) and a column named like the character string given in the on argument, which must be an identifier for the targeted molecule.
• on: [string] Defines the ID that is used to match drugs to their targets. Both supplied data frames (annotation and interaction_table) must contain a column named like this character string.

Returns

A named list. Element target_nodes is a data frame with column node_id (unique node IDs in the iGraph graph object that are 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: elements are drug_names and contain a vector of node IDs that are their specific targets.