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 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | # 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.
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