addPeak2GeneLinks only calculates p2gs in cis?

[RegnerM2015]

Hi @rcorces and @jgranja24

Does the peak-to-gene analysis only focus on peaks that are on the same chromosome as the genes they link to? In other words, is the analysis restricted to links in cis?

I noticed that all of my peak-to-genes links were cis relationships and none were trans (different chromosomes).

[rcorces]

yes - this is implied by maxDist
https://www.archrproject.com/reference/addPeak2GeneLinks.html