populationSimulation: Analyze and graph the average of multiple asynchronous...

In mar-esther23/boolnet-perturb: Perturb Boolean Networks

Description

Analyze and graph the average of multiple asynchronous simulations for an specific number of time steps

Usage

populationSimulation(net, tStates = 1000, simulations = 1000,
  new.nodes = list(), new.values = list(), gene = NULL,
  duration = 1, value = 1, pertTime = 400, onePert = TRUE)

Arguments

net	Boolnet network
tStates	Number of time steps running each simulation, default value set to 1000.
simulations	Number of simulations equivalent to "population size", default value set to 1000.
new.nodes	Nodes to fix with an specific value at the initial state.
new.values	Values for nodes in new.nodes.
gene	Gene to perturb at an specific time-step (pertTime), default value set NULL.
duration	Time of perturbation, default value set to 1.
value	Value of perturbed gene, default value set to 1.
pertTime	Specific time-step at which the gene will be perturbed, default value set to 400.
onePert	If this is TRUE the perturbation will only occur one time during the simulation. If FALSE, de perturbation wil occur periodically, default value set to TRUE.

Value

Data frame with the average of the simulations for each node in each time step

Examples

data(netTh17Treg)
pop_Th17 <- popSimulation(netTh17Treg, new.nodes = c("IL2e","IL21e","TGFBe"), new.values = c(1,1,1), gene ="TGFBe", value = 0)

mar-esther23/boolnet-perturb documentation built on April 21, 2020, 9:11 a.m.