extract_nodes_for_ORA: Extract COSMOS nodes for ORA analysis

In saezlab/COSMOS: COSMOS (Causal Oriented Search of Multi-Omic Space)

Extract COSMOS nodes for ORA analysis

Description

Function to extract the nodes that appear in the COSMOS output network and the background genes (all genes present in the prior knowledge network)

Usage

extract_nodes_for_ORA(sif, att)

Arguments

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

Value

List with 2 objects: the success and the background genes

Examples

CARNIVAL_options <- cosmosR::default_CARNIVAL_options("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)
test_result_for <- format_COSMOS_res(test_result_for)
extreacted_nodes <- extract_nodes_for_ORA(
sif = test_result_for[[1]],
att = test_result_for[[2]]
)

saezlab/COSMOS documentation built on Sept. 17, 2023, 1:22 p.m.