extract_nodes_for_ORA: Extract COSMOS nodes for ORA analysis

View source: R/support_ORA.R

extract_nodes_for_ORAR Documentation

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/cosmosR documentation built on July 27, 2024, 1:30 p.m.