R: Import a network from BioTapestry

loadBioTapestry {BoolNet} | R Documentation

## Import a network from BioTapestry

### Description

Imports a Boolean network from a BioTapestry file (*.btp). BioTapestry is an interactive tool for building, visualizing, and simulating gene-regulatory networks, and can be accessed at http://www.biotapestry.org.

### Usage

    loadBioTapestry(file,
                    symbolic = FALSE)

### Arguments

`file` | The name of the file to import. This must be a BioTapestry XML file (*.btp).
`symbolic` | If set to `TRUE`, the function returns an object of class `SymbolicBooleanNetwork` with an expression tree representation. Otherwise, it returns an object of class `BooleanNetwork` with a truth table representation.

### Details

The function builds up a Boolean network by importing the nodes, the links between these nodes, and the simulation parameters of the top-level plot of a BioTapestry file. The BioTapestry network should have the following properties:

- All links should be either enhancers or repressors. Unspecified ("neutral") links are ignored.

- In the simulation parameters, each node should specify the correct logical function (AND, OR, XOR) for its inputs.

- Constant genes can be generated by modeling a gene without any input link and setting the simulation parameter `initVal` to 0 or 1.

### Value

A network of class `BooleanNetwork` or `SymbolicBooleanNetwork`, as described in `loadNetwork`.

### References

W. J. R. Longabaugh, E. H. Davidson, H. Bolour (2005), Computational representation of developmental genetic regulatory networks. Developmental Biology 283(1):1–16.

### See Also

`loadNetwork`, `loadSBML`

### Examples

    # import the example BioTapestry file
    # included in the package vignette
    exampleFile <- system.file("doc/example.btp",
                               package="BoolNet")
    net <- loadBioTapestry(exampleFile)

    # print the imported network
    print(net)

[Package BoolNet version 2.1.4 Index]