Compute ATM — getATM • diffeRenTES

getATM returns the ATM (Attractor Transition Matrix) structure. The ATM computes the probability of a transition between the attractors of the Boolean network upon the introduction of noise in the form of a logic negation to each node of each state of each attractor, checking in which attractor the dynamics relaxes. The diagonal of the ATM accounts for attractor robustness, as diagonal values represent the probability of returning to the same attractor after a perturbation.

Usage

getATM(net, synchronous_attractors, MAX_STEPS_TO_FIND_ATTRACTORS = 1000)

Arguments

net: The Boolean network previously loaded with loadNetwork() of BoolNet package
synchronous_attractors: Synchronous attractors of the Boolean network
MAX_STEPS_TO_FIND_ATTRACTORS: Number of steps after that the dynamics after the perturbation gives up

Value

The output will be a named list containing the computed ATM structure, the number of the lost flips (i.e., the number of perturbations that have not reach another attractor within the provided MAX_STEPS_TO_FIND_ATTRACTORS), and lastly the attractors in two formats: the one returned by the BoolNet package (called decimal) and their binary translation (called binary).

Examples


net <- BoolNet::generateRandomNKNetwork(10, 2)
attractors <- BoolNet::getAttractors(net)
getATM(net, attractors)
#> $ATM
#>      a1  a2   a3
#> a1 0.50 0.4 0.10
#> a2 0.50 0.4 0.10
#> a3 0.35 0.0 0.65
#> 
#> $lostFLips
#> [1] 0
#> 
#> $attractors
#> $attractors$decimal
#> $attractors$decimal$a1
#> $attractors$decimal$a1$involvedStates
#>      [,1] [,2]
#> [1,]  827  859
#> 
#> $attractors$decimal$a1$basinSize
#> [1] 486
#> 
#> 
#> $attractors$decimal$a2
#> $attractors$decimal$a2$involvedStates
#>      [,1] [,2]
#> [1,]  795  891
#> 
#> $attractors$decimal$a2$basinSize
#> [1] 350
#> 
#> 
#> $attractors$decimal$a3
#> $attractors$decimal$a3$involvedStates
#>      [,1] [,2]
#> [1,]  830  977
#> 
#> $attractors$decimal$a3$basinSize
#> [1] 188
#> 
#> 
#> 
#> $attractors$binary
#> $attractors$binary$a1
#>        [,1] [,2]
#> Gene1     1    1
#> Gene2     1    1
#> Gene3     0    0
#> Gene4     1    1
#> Gene5     1    1
#> Gene6     1    0
#> Gene7     0    1
#> Gene8     0    0
#> Gene9     1    1
#> Gene10    1    1
#> 
#> $attractors$binary$a2
#>        [,1] [,2]
#> Gene1     1    1
#> Gene2     1    1
#> Gene3     0    0
#> Gene4     1    1
#> Gene5     1    1
#> Gene6     0    1
#> Gene7     0    1
#> Gene8     0    0
#> Gene9     1    1
#> Gene10    1    1
#> 
#> $attractors$binary$a3
#>        [,1] [,2]
#> Gene1     0    1
#> Gene2     1    0
#> Gene3     1    0
#> Gene4     1    0
#> Gene5     1    1
#> Gene6     1    0
#> Gene7     0    1
#> Gene8     0    1
#> Gene9     1    1
#> Gene10    1    1
#> 
#> 
#>