format_COSMOS_res {cosmosR} | R Documentation |
formats the network with readable names
format_COSMOS_res( cosmos_res, metab_mapping, gene_mapping = "org.Hs.eg.db", measured_nodes, omnipath_ptm )
cosmos_res |
results of CARNIVAL run |
metab_mapping |
a named vector with pubchem cid as names and desired metabolite names as values. |
gene_mapping |
by default, use the 'org.Hs.eg.db' to map gene names. Can also be a named vector with entrez gene id as names and desired gene names as values. |
measured_nodes |
vector of nodes that are measured or inputs |
omnipath_ptm |
ptms database from OmnipathR |
list with network and attribute tables.
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)