booleanToODE: Translate from Boolean Network to Continuous ODE Network.

Description Usage Arguments Value Examples

View source: R/BNP_BooleanToODE.R

Description

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".

Usage

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

Arguments

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

Value

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.

Examples

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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))

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