Hello,
I am a PhD student working on multi-omics data integration. I am very interested in your Joint Pathway Analysis workflow, using pvalues combination approach, which seems very appropriate. However, some parts remain unclear to me after searching into the code. Regarding the weights vectors (at the pathway level), I was wondering is the ratio was, taking example of metabolites : total_compounds_counts/ total_molecules_counts, or measured_compounds_counts/ total_molecules_counts (meaning: do you take into account the pathway coverage). Secondly, I would like to use this approach to combine pathway scores obtained from ssPA methods (i.e. GSVA, ssGSEA…) coming from different omics. Do you think it could be relevant to apply this kind of procedure directly on pathway scores, instead of pvalues?
Thank you very much in advance for your time.
Best regards,
Gauthier.