I would like to compare several HiC experiments, some prepared with Hind and others with Dpn. I am wondering when is the best time to merge all experiments into a single object?
> param.hind <- pairParam(fragments=hind.fragments)
> param.Dpn <- pairParam(fragments=Dpn.fragments)
> data.Dpn <- squareCounts(input.Dpn, width=1e6, param=param.Dpn)
> data.hind <- squareCounts(input.hind, width=1e6, param=param.hind)
Is it possible/reasonable to merge data.Dpn and data.hind into a data object and continue the workflow?