generateLpFileCarnival: 'generateLpFileCarnival'

In saezlab/CARNIVAL: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

generateLpFileCarnival

Description

generateLpFileCarnival

Usage

generateLpFileCarnival(
  perturbations = NULL,
  measurements,
  priorKnowledgeNetwork,
  weights = NULL,
  carnivalOptions = defaultLpSolveCarnivalOptions()
)

Arguments

perturbations	(optional, if inverse CARNIVAL flavour is used further) vector of targets of perturbations.
measurements	vector of the measurements (i.e. DoRothEA/VIPER normalised enrichment scores)
priorKnowledgeNetwork	data frame of the prior knowledge network
weights	(optional) vector of the additional weights: e.g. PROGENy pathway scores or measured protein activities.
carnivalOptions	the list of options for the run. See defaultLpSolveCarnivalOptions(), defaultCplexCarnivalOptions, defaultCbcCarnivalOptions.

Details

Prepares the input data for the run: tranforms data into lp file and .Rdata file. These files can be reused to run CARNIVAL without preprocessing step using runCarnivalFromLp(..)

Value

paths to .lp file and .RData file that can be used for runFromLpCarnival()

Examples

load(file = system.file("toy_perturbations_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_measurements_ex1.RData",
                        package="CARNIVAL"))
load(file = system.file("toy_network_ex1.RData",
                        package="CARNIVAL"))

## lpSolve
#res1 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
#                             measurements = toy_measurements_ex1,
#                             priorKnowledgeNetwork = toy_network_ex1,
#                             carnivalOptions = defaultLpSolveCarnivalOptions())

#res1["lpFile"] ##path to generated lp file
#res1["parsedDataFile"] ##path to data file used during generation

## Examples for cbc and cplex are commented out because these solvers are not part of R environment
## and need to be installed separately
##
## cbc
## res2 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
##                               measurements = toy_measurements_ex1,
##                               priorKnowledgeNetwork = toy_network_ex1,
##                               carnivalOptions = defaultCbcCarnivalOptions())
##
## res2["lpFile"] ##path to generated lp file
## res2["parsedDataFile"] ##path to data file used during generation
##
## cplex
## res3 = generateLpFileCarnival(perturbations = toy_perturbations_ex1,
##                              measurements = toy_measurements_ex1,
##                              priorKnowledgeNetwork = toy_network_ex1,
##                              carnivalOptions = defaultCplexCarnivalOptions())
##
## res3["lpFile"] ##path to generated lp file
## res3["parsedDataFile"] ##path to data file used during generation

saezlab/CARNIVAL documentation built on Jan. 17, 2024, 5:10 p.m.