perturbState: Perturb network state or trajectory.

Description Usage Arguments Value See Also Examples

View source: R/BNP_PerState.R

Description

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.

Usage

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

Arguments

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.

Value

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)

See Also

stateTransition, getAttractors, perturbTrajectories

Examples

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# 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.

mar-esther23/boolnet-perturb documentation built on Jan. 14, 2019, 7:49 p.m.