loadBioTapestry: Import a network from BioTapestry

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

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 https://biotapestry.systemsbiology.net.

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)

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