make_drug_target: Reformat drug-target-interaction data

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

Description

Function to transform input data to required input format for start_pipeline. Here the data needed to define drug-target interactions is formatted. When the reformatted output is passed to start_pipeline as drug_target_interaction argument, the differential drug response score will be calculated for all the supplied drugs in interaction_table.

Usage

make_drug_target(target_molecules, interaction_table, match_on)

Arguments

target_molecules	Name of layer containing the drug targets. This name has to match the corresponding named item in the list of layers supplied to start_pipeline.
interaction_table	Data frame. Has to contain two columns. Additional columns will be ignored in the pipeline. * A column called 'drug_name' containing names or identifiers of drugs * A column with a name that matches an identifier in the layer supplied in 'target_molecules'. For example, if drugs target proteins and an identifier called 'ncbi_id' was supplied in layer building of the protein layer (make_layer), this column should be called 'ncbi_id' and contain the corresponding IDs of protein-drug targets. Any other ID present in the constructed layer can be used.
match_on	Column name of the data frame supplied in 'interaction_table' that is used for matching drugs and target nodes in the graph (e.g. 'ncbi_id').

Value

Named list of the input parameters in input format of start_pipeline.

Examples

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

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