NetRep

Fast permutation procedure for testing network module replication

An 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.

A preprint is available on BioRxiv: A scalable permutation approach reveals replication and preservation patterns of gene coexpression modules

The main function for this package is modulePreservation. Other useful functions include networkProperties for calculating the topological properties of a module, and plotModule for visualising a gene coexpression network module.

Installation

The latest stable version of this package can be installed directly from this Github repository:

library(devtools)
install_github("InouyeLab/NetRep")

If you have rmarkdown installed, a package vignette (tutorial) is also available to install:

install_github("InouyeLab/NetRep", build_vignettes=TRUE)
vignette("NetRep")

But can otherwise be read online at vignettes/NetRep.md

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

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

Testing the package installation

To ensure the package has installed correctly and will run on your system, run the following:

library(testthat)
test_package("NetRep")

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 fortran and 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.

Some users on OSX Mavericks have reported that even after this step they receive errors relating to -lgfortran or -lquadmath. This is reportedly solved by installing the version of gfortran used to compile the R binary for your system: gfortran-4.8.2, using the following commands in your Terminal application

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

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.