README.md

RandomWalkRestartMH: An R package to perform Random Walk with Restart

Overview

Random Walk with Restart (RWR) is an algorithm developed to provide the distance (or closennes) between nodes in a graph. To do so, RWR simulates an imaginary particle that starts on a seed(s) node(s) and follows randomly the edges of a network. At each step, there is a restart probability, r, meaning that the particle can come back to the seed(s).

This package provides an easy interface to apply RWR on different types of complex networks:

The user can integrate single networks (monoplex networks) to create a multiplex network. The multiplex network can also be integrated, thanks to bipartite relationships, with another multiplex network containing nodes of different nature. Proceeding this way, a network both multiplex and heterogeneous will be generated.

This package was developed in the context of the following publication:

A Valdeolivas, L Tichit, C Navarro, S Perrin, G Odelin, N Levy, P Cau, E Remy, and A Baudot. 2018. “Random walk with restart on multiplex and heterogeneous biological networks.” Bioinformatics 35 (3). DOI: https://doi.org/10.1093/bioinformatics/bty637

Getting Started

RandomWalkRestartMH is available in Bioconductor.

However, we suggest to use devtools to install the latests version from this Github repository with the following command.

## To install the development version from the Github repo:

# install.packages("devtools")
devtools::install_github("alberto-valdeolivas/RandomWalkRestartMH")

Then, we strongly suggest to visit the package website and explore the vignette for a proper usage:

  1. https://alberto-valdeolivas.github.io/RandomWalkRestartMH/

  2. https://alberto-valdeolivas.github.io/RandomWalkRestartMH/articles/RandomWalkRestartMH.html

Citing RandomWalkRestartMH

Please, cite the following publication if you use our package:

A Valdeolivas, L Tichit, C Navarro, S Perrin, G Odelin, N Levy, P Cau, E Remy, and A Baudot. 2018. “Random walk with restart on multiplex and heterogeneous biological networks.” Bioinformatics 35 (3)

Additional Considerations

Please note that this version of the package does not deal with directed networks. New features will be included in future updated versions of RandomWalkRestartMH.



alberto-valdeolivas/RandomWalkRestartMH documentation built on Sept. 7, 2020, 2:19 p.m.