Integrate Phosphoproteomics and transcriptomics studies

Hi saezlab,

Could you please guide me how to integrate phosphoproteomics and transcriptomics data together using CosmosR?

I have generated kinase enrichment using KSEAapp and transcription factors from decoupleR (https://saezlab.github.io/decoupleR/articles/tf_bk.html) using these tutorials. Could you help me how I can include these tools output in cosmosR package. 

Thanks. 