Coexpression

To run the functions “Search Coexpression Group” (code=6) and “Create Network Graph” (code=7), a file containing the coexpression module must be produced.

To create this file, is possible to use the “Coexpression.R” script, which exetutes the WGCNA part 1 tutorial finding the coexpression group of each gene.

This step is not fully automated because a number of steps must be supervised by the user to complete in the best way the analisys.

Moreover there are a few variables that must be modified accoringly to your system and data (eg: number of cores). Up to now, no “interactive” way to modify these variables are implemented: the user must change the values of such variables in the code. This variables are highlighted in the code.

To run the script, simply type:

Rscript coexpression.R

It’s advisable to use this script as a roadmap and conduct the analyses as reported in the official documentation of WGCNA