Thanks for the very nice tool and its precise description in the vignette.
I was wondering if it was possible to use runChicago.R on my data and still be able to perform the downstream QC analyses that you propose, such as <<Visualising interactions>> or <<Peak enrichment for features>>.
Are there any particular runChicago.R output options I should use to be able to do that? and in this case how do I read the output files in R before doing the QC?
Sorry if this is obvious.
Best regards, Sarah Djebali