R package containing functions for assessing the replication/preservation of network topology for weighted gene coexpression network modules in one or more independent datasets through permutation testing.

README.md

NetRep

Fast permutation procedure for testing network module replication

An R package containing functions for assessing the replication and preservation of a network module's topology across datasets through permutation testing. This is suitable for networks that can be meaningfully inferred from multiple datasets. These include gene coexpression networks, protein-protein interaction networks, and microbial interaction networks. Modules within these networks consist of groups of nodes that are particularly interesting: for example a group of tightly connected genes associated with a disease, groups of genes annotated with the same term in the Gene Ontology database, or groups of interacting microbial species, i.e. communities. Application of this method can answer questions such as; (1) do the relationships between genes in a module replicate in an independent cohort? (2) are these gene coexpression modules preserved across tissues or tissue specific? (3) are these modules conserved across species? (4) are microbial communities preseved across multiple spatial locations?

The main function for this package is modulePreservation, which performs the permutation test procedure. Other useful functions include networkProperties for calculating the topological properties of a module, and plotModule for visualising a network module.

For more information see the associated publication in Cell Systems, A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.

Installation

The latest stable version of NetRep can be installed either directly from CRAN or from this GitHub repository:

# From CRAN
install.packages("NetRep")

# Alternatively From GitHub
library(devtools)
install_github("InouyeLab/NetRep")

Developmental / pre-release versions of NetRep can be installed from this repository:

library(devtools)
install_github("InouyeLab/NetRep", ref="devel")

Older versions of NetRep can be installed by specifying the version number in the ref argument:

install_github("InouyeLab/NetRep", ref="v0.61.0")

Package Tutorial

A vignette (tutorial) is available online at vignettes/NetRep.md, or can be loaded directly from R by running vignette("NetRep") if you have installed the package from CRAN.

If you are installing NetRep from GitHub and wish to make the vignette available on your local machine, you will need to install rmarkdown and specify build_vignettes=TRUE when running install_github.

Installation troubleshooting

NetRep and its dependencies require several third party libraries to be installed. If not found, installation of the package will fail.

  1. A compiler with C++11 support for the <thread> libary.
  2. A fortran compiler.
  3. BLAS and LAPACK libraries.

OSX

The necessary C++11 compilers are provided with the Xcode application and subsequent installation of Command line tools. The most recent version of OSX should prompt you to install these tools when installing the devtools package from RStudio. Those with older versions of OSX should be able to install these tools by typing the following command into their Terminal application: xcode-select --install.

The necessary fortran compiler depends on both the OSX version and R version installed by the user. The "R for Mac OS X" page on CRAN provides instructions for determining the correct fortran version as well as relevant download links.

Windows

NetRep can be installed on Windows in R version 3.3.0 or later. The necessary fortran and C++11 compilers are provided with the Rtools program. We recommend installation of NetRep through RStudio, which should prompt the user and install these tools when running devtools::install_github("InouyeLab/NetRep"). You may need to run this command again after Rtools finishes installing.

Linux

If installation fails when compiling NetRep at permutations.cpp with an error about namespace thread, you will need to install a newer version of your compiler that supports this C++11 feature. We have found that this works on versions of gcc as old as gcc-4.6.3.

If installation fails prior to this it is likely that you will need to install the necessary compilers and libraries, then reinstall R. For C++ and fortran compilers we recommend installing g++ and gfortran from the appropriate package manager for your operating system (e.g. apt-get for Ubuntu). BLAS and LAPACK libraries can be installed by installing libblas-dev and liblapack-dev. Note that these libraries must be installed prior to installation of R.