drug_target_edges_example: Drug target nodes in combined network

In DrDimont: Drug Response Prediction from Differential Multi-Omics Networks

Drug target nodes in combined network

Description

Exemplary intermediate pipeline output: Drug targets detected in the combined graphs. A named list with elements 'targets' and 'edgelists'. This was created with determine_drug_targets using the combined_graphs_example and:

Usage

drug_target_edges_example

Format

A named list with 2 items.

targets

A named list

target_nodes

data frame with column 'node_id' (unique node IDs in the graph targeted by drugs) and columns 'groupA' and 'groupB' (bool values specifying whether the node is contained in the combined graph of the group)

drugs_to_target_nodes

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 data frame of edges adjacent to drug target nodes each. Each edgelist data frame contains columns 'from', 'to' and 'weight'.

Details

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

Drug-gene interactions to calculate this output were used from The Drug Gene Interaction Database.

Source

The Drug Gene Interaction Database: https://www.dgidb.org/

DrDimont documentation built on Sept. 23, 2022, 5:06 p.m.