check_input function

Check pipeline input data for required format

Checks if input data is valid and formatted correctly. This function is a wrapper for other check functions to be executed as first step of the DrDimont pipeline.

check_input(layers, inter_layer_connections, drug_target_interactions)

Arguments

• layers: [list] List of layers to check. Individual layers were created by make_layer and need to be wrapped in a list.
• inter_layer_connections: [list] A list containing connections between layers. Each connection was created by make_connection and wrapped in a list.
• drug_target_interactions: [list] A named list of the drug interaction data. Created by make_drug_target

Returns

Character string vector containing error messages.

Examples

data(layers_example)
data(metabolite_protein_interactions)
data(drug_gene_interactions)
data

all_layers <- layers_example

all_inter_layer_connections = list(
    make_connection(from='mrna', to='protein', connect_on='gene_name', weight=1),
    make_connection(from='protein', to='phosphosite', connect_on='gene_name', weight=1),
    make_connection(from='protein', to='metabolite',
    connect_on=metabolite_protein_interactions, weight='combined_score'))

all_drug_target_interactions <- make_drug_target(
                                    target_molecules="protein",
                                    interaction_table=drug_gene_interactions,
                                    match_on="gene_name")

return_errors(check_input(layers=all_layers,
    inter_layer_connections=all_inter_layer_connections,
    drug_target_interactions=all_drug_target_interactions))