isInputValidCarnival: Checks validity of all inputs of CARNIVAL

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

Checks validity of all inputs of CARNIVAL

Description

Checks validity of all inputs of CARNIVAL

Usage

isInputValidCarnival(
  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.

Value

TRUE if everything passed the checks.

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
#isInputValidCarnival(perturbations = toy_perturbations_ex1,
#                    measurements = toy_measurements_ex1,
#                    priorKnowledgeNetwork = toy_network_ex1,
#                    carnivalOptions = defaultLpSolveCarnivalOptions())

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