perturbState: Perturb network state or trajectory.
In mar-esther23/boolnet-perturb: Perturb Boolean Networks

Description Usage Arguments Value See Also Examples

Modifies the values of a state and returns the resulting attractor or trajectory. If time=NULL the perturbation will be fixed permanently, if time=n the perturbation will last n time steps and then the rules will return to their original values.

1 2	perturbState(net, state, genes, time = 1, result = c("attractor", "nextState", "trajectory"), all.data = F, int = F, ...)

`net`	BoolNet network to perturb
`state`	state to perturb, default is a random state.
`genes`	genes to perturb, default is a random gene.
`time`	time of perturbation, default is 1. If time=NULL the perturbation will be fixed permanently, if time=n the perturbation will last n time steps and then the rules will return to their original values.
`result`	select 'attractor','nextState','trajectory'
`all.data`	returns list with initial state, perturb node, and result. states will be simplified as integer or string with sep='/' for cycles
`int`	return attractor as int with sep="/"
`...`	Further parameters to `stateTransition` and `getAttractors`.
`values`	value of perturbed genes, default is bitflip of target genes.

If result='attractor' returns the attractor the state reached after the perturbation if result=”nextState' returns the next state reached after the perturbation if result='trajectory' return the trajectory after perturbation (only synchronous update)

stateTransition, getAttractors, perturbTrajectories

# Perturb two nodes of a state for one time step, return attractor object
> perturbState(cellcycle, 162, c('CycD', 'Rb'))
 |--<---------|
 V            |
 0100010100   |
 V            |
 |-->---------|

# Perturb two nodes of a state for one time step, return nextState
> perturbState(cellcycle, 162, c('CycD', 'Rb'), result='nextState')
  CycD     Rb    E2F   CycE   CycA    p27  Cdc20   Cdh1 UbcH10   CycB 
     0      0      1      0      0      0      0      1      0      0 

# Perturb an state by permanetly fixing the value of nodes, return the trajectory
> perturbState(cellcycle, 162, c('CycD', 'Rb'), result = 'trajectory')
  CycD Rb E2F CycE CycA p27 Cdc20 Cdh1 UbcH10 CycB
1    0  1   0    0    0   1     0    1      0    0
2    1  0   0    0    0   1     0    1      0    0
3    0  0   1    0    0   0     0    1      0    0
4    0  1   1    1    1   1     0    1      0    0
5    0  1   0    0    0   0     0    1      0    0
6    0  1   0    0    0   1     0    1      0    0

# Perturb random node for 3 time steps
perturbState(cellcycle, time=3)

Modify state, set new value to target nodes.