BoolNet (version 2.1.9)

fixGenes: Simulate knocked-out or over-expressed genes

Description

Simulates knocked-out or over-expressed genes by fixing the values of genes to 0 or 1, or turn off knock-out or over-expression of genes.

Usage

fixGenes(network, fixIndices, values)

Value

Depending on the input, an object of class BooleanNetwork, SymbolicBooleanNetwork or ProbabilisticBooleanNetwork containing the fixed genes is returned. These classes are described in more detail in loadNetwork.

Arguments

network

The original network of class BooleanNetwork, SymbolicBooleanNetwork or ProbabilisticBooleanNetwork containing the genes to be fixed

fixIndices

A vector of names or indices of the genes to be fixed

values

Either one single value, or a vector with the same length as fixIndices. For each gene, a value of 1 means that the gene is always turned on (over-expressed), a value of 0 means that the gene is always turned off (knocked-out), and a value of -1 means that the gene is not fixed.

See Also

loadNetwork

Examples

if (FALSE) {
# load example data
data(cellcycle)

# knock out gene CycD (index 1)
net <- fixGenes(cellcycle, 1, 0)
# or
net <- fixGenes(cellcycle, "CycD", 0)

# get attractors by exhaustive search
attractors <- getAttractors(net)

print(attractors)
}