computeFc {bnem} | R Documentation

## Compute differential effects

### Description

computes differential effects given an activation pattern (absolute gene expression or truth table)

### Usage

    computeFc(CNOlist, y)

### Arguments

`CNOlist` | CNOlist object (see package CellNOptR), if available.
`y` | activation pattern according to the annotation in CNOlist

### Value

numeric matrix with annotated response scheme

### 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"))
    model <- CellNOptR::preprocessing(CNOlist, PKN, maxInputsPerGate = 100)
    expression <- matrix(rnorm(nrow(slot(CNOlist, "cues"))*10), 10,
    nrow(slot(CNOlist, "cues")))
    fc <- computeFc(CNOlist, expression)

[Package bnem version 1.2.0 Index]