ORA (Pathway analysis)

[ChristinaSchmidt1]

here we need two things:

1. Standard: use decoupleR?
2. On MCA --> ORA --> script I already made

[ChristinaSchmidt1]

I checked with Pau and in the R version of decoupleR there is not the option I need for ORA to be usable on the metabolite clutsers from MCA. Hence I have used enrichR for this. Advantage here is that this automatically generates some plots for us.

Next I will also need to:

1. Pathway analysis function to be usable with the DMA output DM_ORA() --> Here we could consider to use decoupleR instead and either write a wrapper or have a function that add the pathway information needed for the plots
2. Add a pathway analysis function to be usable with the DMA output from CoRe --> must be ORA, as we need to use groups not only based on tval, but also based on the info if it was released/consumed
3. Update Figure 1 to accomondate this new module

[ChristinaSchmidt1]

Add the KEGG pathways I have generated for MetSigDB into package to run pathway analysis. Later we can always update this with direct accessing MetSigDB/OmniPath to choose from pathways and convert IDs internally. For now, I would just use the standard pathways, so we can push this forward.