fixGenes: Simulate knocked-out or over-expressed genes

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

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, 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.

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.

See Also

loadNetwork

Examples

## Not run: 
# 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)

## End(Not run)

BoolNet documentation built on Oct. 2, 2023, 5:08 p.m.