computeFc: Compute differential effects

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

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)

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