WGCNA

Author

Cox Lab

Published

November 15, 2023

1 Weighted Gene Co-expression Network Analysis

This package is provided through the R-language integration into Perseus and therefore requires R as well as the package itself to be installed in order to be used. Visit the PluginInterop and PerseusR for additional technical information on the integration of R and Perseus.

2 Installation

  • Download the R installer install it.
  • Remember the R installation directory. If you do not know where you have installed R, check the default location C:\Program Files\R\R-3.5.0\bin, or search for Rscript.exe.
  • Add R to your Path environment variable. Open the start menu and search for “environment variables”, and select “Edit system environment variables”.
  • Find the Path variable in the editor and select Edit.
  • Now we can add R to the Path by clicking New and entering the location of the .../bin folder of the R installation, e.g C:\Program Files\R\R-3.5.0\bin.
  • In certain Windows version you might have to edit the Path directly. The Path consists of folder locations separated by ‘;’. Therefore, just append the installation location of R and the ‘;’ separator. No spaces or quotes are required. If the Path variable is not defined on your system, you can define it yourself.
  • Check that R is installed correctly by opening cmd.exe from the start menu and entering R An R session should start.
  • Inside the running R session, install the WGCNA and PerseusR libraries by entering/pasting the following code line-by-line. When prompted for local install, type ‘yes’ twice and select a close-by server for the package download.
# | eval: false
install.packages("BiocManager")
BiocManager::install(c("WGCNA", "devtools"))
library(devtools)
install_github('jdrudolph/PerseusR')
  • You should now be able to load the WGCNA and PerseusR libraries by entering the following code. Upon loading, WGCNA will print some output, while PerseusR will not print any.
# | eval: false
library(WGCNA)
library(PerseusR)

You are now ready to perform co-expression analysis from within Perseus.

3 WGCNA functions