Hello, Given very sparse definition, it seems you are trying to simply constructy a network object, useful for further analysis.
- Obtain edges between genes based on expression
- Compute properties of the network
The first step is an active research area. I would suggest you look at: https://bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html for starters.
The second step highly depends on what you are trying to achieve. Please describe that in a bit more detail.