R: Simulate knocked-out or over-expressed genes

fixGenes {BoolNet} | R Documentation

## 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

    # 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)

[Package BoolNet version 2.1.4 Index]