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

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

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

Author

Leshi Chen, leshi, chen@lincolnuni.ac.nz, chenleshi@hotmail.com

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)
#> Discovered Attractors via Fundamental Boolean Model :
#> Genes are encoded in the following order::
#> Gene1 Gene2 Gene3 Gene4 Gene5:
#> 
#> Attractor 1 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 0 0 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 2 is a complex attractor consisting of 4 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 0 0 0       |
#> |               |
#> 1 0 0 0 1       |
#> |               |
#> 1 1 0 0 1       |
#> |               |
#> 1 1 0 0 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 3 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 1 1 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 4 is a complex attractor consisting of 5 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 1 1 1       |
#> |               |
#> 1 0 1 0 1       |
#> |               |
#> 1 1 1 0 1       |
#> |               |
#> 1 1 1 0 0       |
#> |               |
#> 1 0 1 1 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
FBNNetwork.Graph.DrawAttractor(NETWORK2,attractor,3)


## find attractor with type = asynchronous
attractor <- searchForAttractors(NETWORK2,
                               initialStates,
                               type = 'asynchronous',
                               ExampleNetwork$genes)
print(attractor)
#> Discovered Attractors via Fundamental Boolean Model :
#> Genes are encoded in the following order::
#> Gene1 Gene2 Gene3 Gene4 Gene5:
#> 
#> Attractor 1 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 0 0 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 2 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 0 0 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 3 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 1 0 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 4 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 1 0 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 5 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 0 1 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 6 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 0 1 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 7 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 1 1 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 8 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 1 1 0       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 9 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 0 0 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 10 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 1 0 0 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 11 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 1 0 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 12 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 1 1 0 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 13 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 0 1 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 14 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 0 1 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 15 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 0 0 1 1 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
#> Attractor 16 is a simple attractor consisting of 1 state(s):
#> 
#> | --< - - - - - |
#> v               ^
#> 1 0 1 1 1       |
#> |               |
#> v               ^
#> | - - - - - >-- |
#> 
#> 
FBNNetwork.Graph.DrawAttractor(NETWORK2,attractor,3)