extract_nodes_for_ORA {cosmosR} | R Documentation |
Function to extract the nodes that appear in the COSMOS output network and the background genes (all genes present in the prior knowledge network)
extract_nodes_for_ORA(sif, att)
sif |
df; COSMOS network solution in sif format like the first list element returned by the format_cosmos_res function |
att |
df; attributes of the nodes of the COMSOS network solution like the second list element returned by the format_cosmos_res function |
List with 2 objects: the success and the background genes
CARNIVAL_options <- cosmosR::default_CARNIVAL_options() CARNIVAL_options$solver <- "lpSolve" data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = CARNIVAL_options ) test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for, CARNIVAL_options = CARNIVAL_options) data(metabolite_to_pubchem) data(omnipath_ptm) test_result_for <- format_COSMOS_res(test_result_for, metab_mapping = metabolite_to_pubchem, measured_nodes = unique(c(names(toy_metabolic_input), names(toy_signaling_input))), omnipath_ptm = omnipath_ptm) extreacted_nodes <- extract_nodes_for_ORA( sif = test_result_for[[1]], att = test_result_for[[2]] )