make_drug_target {DrDimont} | R Documentation |
Reformat drug-target-interaction data
Description
Function to transform input data to required input format for
run_pipeline
. Here the data that is needed to define drug-target interactions is
formatted. When the reformatted output is passed to run_pipeline
as
drug_target_interactions
argument, the differential integrated drug response score can be
calculated for all the supplied drugs in interaction_table
.
Usage
make_drug_target(target_molecules, interaction_table, match_on)
Arguments
target_molecules |
[string] Name of layer containing the drug targets. This name has to match the
corresponding named item in the list of layers supplied to |
interaction_table |
[data.frame] Has to contain two columns. A column called 'drug_name' containing
names or identifiers of drugs. And a column with a name that matches an identifier in the layer supplied
in 'target_molecules'. Additional columns will be ignored in the pipeline.
For example, if drugs target proteins and an identifier called 'ncbi_id' was supplied in layer creation of
the protein layer (see |
match_on |
[string] 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 run_pipeline
.
Examples
data(drug_gene_interactions)
example_drug_target_interactions <- make_drug_target(target_molecules='protein',
interaction_table=drug_gene_interactions,
match_on='gene_name')