simulateStatesRecursive {bnem} | R Documentation |
simulates the activation pattern (truth table) of a hyper-graph and annotated perturbation experiments
simulateStatesRecursive(CNOlist, model, bString, NEMlist = NULL)
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 |
return the truth tables for certain perturbation experiments as a numeric matrix
Martin Pirkl
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)))