run_COSMOS_metabolism_to_signaling: run COSMOS metabolism to signaling

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

run COSMOS metabolism to signaling

Description

Runs COSMOS from metabolism to signaling. This function uses CARNIVAL to find a subset of the prior knowledge network based on optimization that (1) includes the most measured and input nodes and (2) which is in agreement with the data. Use preprocess_COSMOS_metabolism_to_signaling to prepare the the inputs, measurements and the prior knowledge network.

Usage

run_COSMOS_metabolism_to_signaling(
  data,
  CARNIVAL_options = default_CARNIVAL_options("lpSolve")
)

Arguments

data	cosmos_data object. Use the preprocess_COSMOS_metabolism_to_signaling function to create an instance.
CARNIVAL_options	List that controls the options of CARNIVAL. See details in default_CARNIVAL_options.

Value

List with the following elements:

weightedSIF

The averaged networks found by optimization in a format of a Simple Interaction network, i.e. each row codes an edge

N_networks

Number of solutions found by the optimization

nodesAttributes

Estimated node properties

individual_networks

List of optimial networks found

individual_networks_node_attributes

Node activity in each network

See Also

preprocess_COSMOS_metabolism_to_signaling, runCARNIVAL, cosmos_data

Examples

data(toy_network)
data(toy_signaling_input)
data(toy_metabolic_input)
data(toy_RNA)
test_back <- preprocess_COSMOS_metabolism_to_signaling(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 = default_CARNIVAL_options("lpSolve"))

test_result_back <- run_COSMOS_metabolism_to_signaling(data = test_back,
                       CARNIVAL_options = default_CARNIVAL_options("lpSolve"))

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