constructFBNCube: Create an Orchard cube

In clsdavid/FBNNet2_public: Fundamental Boolean Model and Networks

Create an Orchard cube

Description

This is the main function(s) to genereate a single Orchard Cube or a group of cubes

Usage

constructFBNCube(
  target_genes,
  conditional_genes,
  timeseriesCube,
  maxK = 5,
  temporal = 1,
  useParallel = FALSE
)

Arguments

target_genes	A vector of genes that will be treated as target genes
conditional_genes	All genes that are available for building up the cube
timeseriesCube	A list of samples in which a sample is a matrix that contains gene states where genes in rows and time points in columns.
maxK	The maximum level the cube can dig in
temporal	A value that used to be 1 indicates the previous steps the current one can depend on
useParallel	If it is TRUE, the constructing will run it in parallel, otherwise in a singl thread

Value

An Orchard cube that contains all precomputed measures

Examples

require(BoolNet)
data('ExampleNetwork')
initialStates <- generateAllCombinationBinary(ExampleNetwork$genes)
trainingseries <- genereateBoolNetTimeseries(ExampleNetwork,
                                           initialStates,
                                           43,
                                           type='synchronous')
cube<-constructFBNCube(target_genes = ExampleNetwork$genes,
                       conditional_genes = ExampleNetwork$genes,
                       timeseriesCube = trainingseries,
                       maxK = 4,
                       temporal = 1,
                       useParallel = FALSE)
network <- mineFBNNetwork(cube,ExampleNetwork$genes)
network
## draw the general graph
FBNNetwork.Graph(network)

clsdavid/FBNNet2_public documentation built on April 20, 2023, 4:36 p.m.