dummyCNOlist {bnem} | R Documentation |
creates a general CNOlist object from meta information
dummyCNOlist( stimuli = NULL, inhibitors = NULL, maxStim = 0, maxInhibit = 0, signals = NULL )
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. |
CNOlist object
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, signals = c("A", "B","C","D"))