BoolNet (version 2.1.5)

loadBioTapestry: 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)

Value

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

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.

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)