simulateStatesRecursive: Simulate states

In MartinFXP/B-NEM: Training of logical models from indirect measurements of perturbation experiments

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)))

MartinFXP/B-NEM documentation built on Nov. 5, 2024, 11:56 a.m.