BoolNet (version 1.44)

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)

Arguments

network

The original network of class BooleanNetwork or latex{ }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

Value

• Depending on the input, an object of class BooleanNetwork or ProbabilisticBooleanNetwork containing the fixed genes is returned. The classes BooleanNetwork and latex{ }ProbabilisticBooleanNetwork is described in more detail in loadNetwork.

See Also

loadNetwork

Examples

library(BoolNet)

# 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)