simulateStatesRecursive {bnem} | R Documentation

## Simulate states

### Description

simulates the activation pattern (truth table) of a hyper-graph and annotated perturbation experiments

### Usage

    simulateStatesRecursive(CNOlist, model, bString, NEMlist = NULL)

### Arguments

`CNOlist` | CNOlist object (see package CellNOptR), if available.
`model` | Model object including the search space, if available. See CellNOptR::preprocessing.
`bString` | binary vector denoting the sub-graph given model
`NEMlist` | NEMlist object only for devel

### Value

return the truth tables for certain perturbation experiments as a numeric matrix

### Author(s)

Martin Pirkl

### Examples

    sifMatrix <- rbind(c("A", 1, "B"), c("A", 1, "C"), c("B", 1, "D"),
    c("C", 1, "D"))
    temp.file <- tempfile(pattern="interaction",fileext=".sif")
    write.table(sifMatrix, file = temp.file, sep = "\t",
    row.names = FALSE, col.names = FALSE,
    quote = FALSE)
    PKN <- CellNOptR::readSIF(temp.file)
    CNOlist <- dummyCNOlist("A", c("B","C","D"), maxStim = 1, maxInhibit = 2,
    signal = c("A", "B","C","D"))
    model <- CellNOptR::preprocessing(CNOlist, PKN, maxInputsPerGate = 100)
    states <- simulateStatesRecursive(CNOlist, model,
    rep(1, length(model$reacID)))

[Package bnem version 1.0.0 Index]