GraphAlignment (R package)

1.0.0

Introduction

GraphAlignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. This package implements the Bayesian scoring methods and the alignment algorithm introduced in the paper J. Berg and M. Lässig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006). Documentation and installation guide are available below.

Releases

See the Bioconductor GraphAlignment page for the latest releases of the package (including precompiled OS X and Windows binaries) and documentation downloads:

http://bioconductor.org/packages/2.2/bioc/html/GraphAlignment.html

Installation

The GraphAlignment package can be installed using the standard R package installation procedure. If you have downloaded a release tarball of the package (named, for example, GraphAlignment_1.0-0.tar.gz), use the following command line to install in the specified location:

R CMD INSTALL PATH_TO_PACKAGE --library=R_EXTENSION_PATH

PATH_TO_PACKAGE is the relative or absolute path to the package tarball (for example GraphAlignment_1.0-0.tar.gz or /home/someuser/downloads/GraphAlignment_1.0-0.tar.gz). R_EXTENSION_PATH is the path where the package should be installed. This option may be omitted if you intend to install the package in the default location.

Otherwise, if you have downloaded a snapshot release or got the latest development version from the respository, change to the directory which contains the (unpacked and untarred) GraphAlignment distribution directory (named GraphAlignment) and type

R CMD INSTALL GraphAlignment --library=R_EXTENSION_PATH

Please note that since GraphAlignment is a source package, a working R command line interface and build tools such as a bash compatible shell, make and a C compiler are required for installation.

Usage

The package can be imported into the R workspace as follows:

library("GraphAlignment", lib.loc="R_EXTENSION_PATH")

Where R_EXTENSION_PATH is the path where the package has been installed. The extension path may be omitted if the package has been installed in the default location.

Documentation

The GraphAlignment package provides two types of documentation: Documentation for the R user interface and API documentation for the C implementation of some of the features provided by the package.

The user manual for the package is available in PDF format here.

Documentation for the functions provided by the package is available through the built-in help system of the R programming environment, usually by typing help(<function name>) or ?<function name>, where <function name> is the name of a function which is provided by the GraphAlignment package.

The user documentation generated by R can also be browsed online in HTML format here.

A current version of the code documentation is available online at http://www.thp.uni-koeln.de/~berg/GraphAlignment/.

License

Authors: Jörn P. Meier (mail@ionflux.org), Michal Kolář, Ville Mustonen, Michael Lässig, and Johannes Berg.

The package can be used freely for non-commercial purposes. If you use this package, the appropriate paper to cite is J. Berg and M. Lässig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006), available from http://www.pnas.org/cgi/content/full/103/29/10967.

This software is made available in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

This software contains code for solving linear assignment problems which was written by Roy Jonker, MagicLogic Optimization Inc.. Please note that this code is copyrighted, © 2003 MagicLogic Systems Inc., Canada and may be used for non-commercial purposes only. See http://www.magiclogic.com/assignment.html for the latest version of the LAP code and details on licensing.


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