mineFBNNetwork: Mine FBN Networks from an Orchard cube

In clsdavid/FBNNet2_public: Fundamental Boolean Model and Networks

Mine FBN Networks from an Orchard cube

Description

Mine FBN Networks from an Orchard cube

Usage

mineFBNNetwork(
  fbnGeneCube,
  genes = NULL,
  useParallel = FALSE,
  threshold_confidence = 1,
  threshold_error = 0,
  threshold_support = 1e-05,
  maxFBNRules = 5
)

Arguments

fbnGeneCube	A pre constructed Orchard cube
genes	The target genes in the output
useParallel	An option turns on parallel
threshold_confidence	A threshold of confidence (between 0 and 1) that used to filter the Fundamental Boolean functions
threshold_error	A threshold of error rate (between 0 and 1) that used to filter the Fundamental Boolean functions
threshold_support	A threshold of support (between 0 and 1) that used to filter the Fundamental Boolean functions
maxFBNRules	The maximum rules per type (Activation and Inhibition) per gene can be mined or filtered, the rest will be discarded

Value

A object of FBN network

Author(s)

Leshi Chen, leshi, [e-mail]

References

Chen et al.(2018), Front. Physiol., 25 September 2018, (Front. Physiol.)

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

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