Extracting Co-expression Matrices for Each Condition from hdWGCNA Consensus Network

[TemiLeke]

Hi team,

I've recently started using the hdWGCNA package and have been working with the consensus network analysis.

I'm interested in extracting the co-expression matrices for each of the conditions from the group where I constructed a consensus network. Is there a recommended method or procedure to achieve this within the package?

Thanks a lot!

[smorabit]

Hi,

At this time, the individual co-expression networks are not saved when you run consensus network analysis. This sounds like it could be an interesting addition, and I can start to work on a solution to provide this result (not sure when that will be done). In the mean time, a workaround could be just running hdWGCNA individually on each of your groups and then using the GetTOM function to extract the co-expression matrix.

[TemiLeke]

Thanks for your reply!

Certainly, it would be an interesting addition. It hadn't occurred to me to use hdWGCNA on each group. My initial impression was that there might be an inconsistency. Given that the ConsensusNetwork function invokes the WGCNA blockwiseConsensusModules function, which in turn calls the blockwiseIndividualTOMs function, I attempted to modify the removeIndividualTOMsOnExit parameter to TRUE. This would allow saving the individual TOMs. However, since this parameter seems to be set to true by default, the individual TOMs are automatically deleted. To fix this, I made custom modifications to a forked version of WGCNA. I'm uncertain if this approach might prove useful in future implementations.