reduceGraph: Reduce graph

In MartinFXP/bnem: Training of logical models from indirect measurements of perturbation experiments

Reduce graph

Description

reduces the size of a graph, if possible, to an equivalent sub-graph

Usage

reduceGraph(bString, model, CNOlist)

Arguments

bString	binary vector indicating the sub-graph given a model
model	Model object including the search space, if available. See CellNOptR::preprocessing.
CNOlist	CNOlist object (see package CellNOptR), if available.

Value

equivalent sub-graph denoted by a bString

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)
bString <- reduceGraph(rep(1, length(model$reacID)), model, CNOlist)

MartinFXP/bnem documentation built on Nov. 5, 2024, 11:57 a.m.