dummyCNOlist: Create dummy CNOlist

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

Create dummy CNOlist

Description

creates a general CNOlist object from meta information

Usage

dummyCNOlist(
  stimuli = NULL,
  inhibitors = NULL,
  maxStim = 0,
  maxInhibit = 0,
  signals = NULL
)

Arguments

stimuli	Character vector of stimuli names.
inhibitors	Character vector of inhibitors.
maxStim	maximal number of stimulated genes for a single experiment
maxInhibit	maximal number of inhibited genes for a single experiment
signals	Optional character vector of signals. Signals are S-genes, which can directly regulate E-genes. If left NULL, all stimuli and inhibitors are defined as signals.

Value

CNOlist object

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,
signals = c("A", "B","C","D"))

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