molnet (version 0.1.0)

make_drug_target: Reformat drug-target-interaction data

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

# NOT RUN {
data(drug_gene_interactions)
drug_target_interaction <- make_drug_target(target_molecules='protein',
interaction_table=drug_gene_interactions, match_on='gene_name')

# }