booleanToODE: Translate from Boolean Network to Continuous ODE Network.
In mar-esther23/boolnet-perturb: Perturb Boolean Networks

Description Usage Arguments Value Examples

The function translate the Boolean Network to a Determinist Continuous Network composed by two principal parts. The first one containes the translation from classic to fuzzy logic using one of two methods. The second one contains an ODE-based description of the rate of changes for each of the nodes. IMPORTANT: This function call the perl script "ConvertTocontinuos.pl".

1 2	booleanToODE(net, logic = "Zadeh", eq = "SQUAD", sep = ",", mutants = c(), keep.input = FALSE)

`net`	BoolNet network
`logic`	is a character string specificating either if Zadeh or Probabilistic logic is employed during the translation. Default: Zadeh.
`eq`	is a character string specificating either if the equation proposed by Sanchez-Corrales et al., 2010 or Villarreal et al., 2012 is employed by describe the rate of change for the nodes in the network.
`sep`	between targets and factors in file, default ","
`mutants`	list of genes to mutate, the derivate will be 0
`keep.input`	if TRUE set the derivate of the inputs to 0

Returns a list with func (ode function), parameters and example state and time. The parameters are a vector where h=10, w=0.5 and decay rate = 1.

library(deSolve)
data(cellcycle)

net.ode <- booleanToODE(cellcycle)
ode(func = net.ode$func, 
    parms = net.ode$parameters, 
    y = net.ode$state, 
    times = seq(0, 5, 0.1))