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.

run_COSMOS_metabolism_to_signaling(
  data,
  CARNIVAL_options = default_CARNIVAL_options()
)

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

Examples

CARNIVAL_options <- cosmosR::default_CARNIVAL_options() CARNIVAL_options$solver <- "lpSolve" 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 = CARNIVAL_options )
#> 'select()' returned 1:1 mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> [1] "COSMOS: all 2 signaling nodes from data were found in the meta PKN" #> [1] "COSMOS: all 3 metabolic nodes from data were found in the meta PKN" #> [1] "COSMOS: 4653 of the 15919 genes in expression data were found as transcription factor target" #> [1] "COSMOS: 4653 of the 5303 transcription factor targets were found in expression data" #> [1] "COSMOS: removing unexpressed nodes from PKN..." #> [1] "COSMOS: 0 interactions removed" #> [1] "COSMOS: removing nodes that are not reachable from inputs within 15 steps" #> [1] "COSMOS: 1 from 19 interactions are removed from the PKN" #> [1] "COSMOS: 1 input/measured nodes are not in PKN any more: X2305 and 0 more." #> [1] "COSMOS: removing nodes that are not observable by measurements within 15 steps" #> [1] "COSMOS: 11 from 18 interactions are removed from the PKN" #> [1] "COSMOS: 2 input/measured nodes are not in PKN any more: XMetab__124886___c____, XMetab__6426851___c____ and 0 more." #> [1] "COSMOS: 0 interactions are removed from the PKN based on consistency check between TF activity and gene expression" #> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers." #> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
#> Writing constraints...
#> Solving LP problem...
#> #> ── Column specification ──────────────────────────────────────────────────────── #> cols( #> `enter Problem` = col_character() #> )
#> [1] "COSMOS: 0 interactions are removed from the PKN based on consistency check between TF activity and gene expression" #> [1] "COSMOS: all 1 signaling nodes from data were found in the meta PKN" #> [1] "COSMOS: all 1 metabolic nodes from data were found in the meta PKN" #> [1] "COSMOS: 4653 of the 15919 genes in expression data were found as transcription factor target" #> [1] "COSMOS: 4653 of the 5303 transcription factor targets were found in expression data"
test_result_back <- run_COSMOS_metabolism_to_signaling(data = test_back, CARNIVAL_options = CARNIVAL_options)
#> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
#> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign().
#> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."
#> Writing constraints...
#> Solving LP problem...
#> #> ── Column specification ──────────────────────────────────────────────────────── #> cols( #> `enter Problem` = col_character() #> )