promoter-promoter and enh-promoter interactions

[Abeer-hes]

Hello

Thanks for this great package and sorry for the simple question in advance.
I want to ask regarding the predications, if I include promoters in the makecandidateregions module, would I get gene-gene interactions, and would that make my enhancers-genes interactions less in favor compared to the case if I run the modules from only ATAC-seq peaks (if I am using the same threshold). I am interested in both interactions.
What would you suggest to include both? would it be okay to run the modules from identifying the candidate regions onward using different list (one including ATAC peaks, the other peaks+promoters) or should I lower the threshold of the prediction.
Thanks a lot.