| 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)