searchForAttractors: A function to find all possible FBM (Fundamental Boolean...

In clsdavid/FBNNet2_public: Fundamental Boolean Model and Networks

A function to find all possible FBM (Fundamental Boolean models) attractors

Description

A function to find all possible FBM (Fundamental Boolean models) attractors

Usage

searchForAttractors(
  fbnNetwork,
  startStates = list(),
  genes,
  type = c("synchronous", "asynchronous"),
  genesOn = c(),
  genesOff = c(),
  maxSearch = 1000
)

Arguments

fbnNetwork	An object of FBNNetwork
startStates	A list of initial states, the row names of each state must be matched with the genes
genes	a list of genes which index order must match with the current state
type	A type of Boolean network update schema chosen from synchronous, asynchronous and time step based
genesOn	It is a vector of genes that are marked as On
genesOff	It is a vector of genes that are marked as Off
maxSearch	The maximum timesteps that the system will try to search.

Value

Attractor objects

Author(s)

Leshi Chen, leshi, [e-mail], [e-mail]

References

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

Mussel, Hopfensitz et al. 2010, BoolNet - an R package for generation, reconstruction and analysis of Boolean networks

Examples

data('ExampleNetwork')
initialStates <- generateAllCombinationBinary(ExampleNetwork$genes)
trainingseries <- genereateBoolNetTimeseries(ExampleNetwork,
                                           initialStates,
                                           43,
                                           type='synchronous')
cube<-constructFBNCube(target_genes = ExampleNetwork$genes,
                       conditional_genes = ExampleNetwork$genes,
                       timeseriesCube = trainingseries,
                       maxK = 4,
                       temporal = 1,
                       useParallel = FALSE)
NETWORK2 <- mineFBNNetwork(cube,ExampleNetwork$genes)

## find attractor with type = synchronous
attractor <- searchForAttractors(NETWORK2,
                               initialStates,
                               ExampleNetwork$genes)
print(attractor)
FBNNetwork.Graph.DrawAttractor(NETWORK2,attractor,3)

## find attractor with type = asynchronous
attractor <- searchForAttractors(NETWORK2,
                               initialStates,
                               type = 'asynchronous',
                               ExampleNetwork$genes)
print(attractor)
FBNNetwork.Graph.DrawAttractor(NETWORK2,attractor,3)

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