format_COSMOS_res {cosmosR}R Documentation

format_COSMOS_res

Description

formats the network with readable names

Usage

format_COSMOS_res(
  cosmos_res,
  metab_mapping,
  gene_mapping = "org.Hs.eg.db",
  measured_nodes,
  omnipath_ptm
)

Arguments

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

Value

list with network and attribute tables.

Examples

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)

[Package cosmosR version 1.0.1 Index]