should I merge regions across samples in permutation testing with regioneR
I have regions of mutational events across multiple samples, some of which are recurrent (the same part of the genome is mutated across multiple samples).
I want to see if these regions overlap a set of putative regulatory elements more than by chance using regioneR.
Should I merge the regions across multiple samples so each region is only counted once? Or should I account for the fact that some regions are recurrent and therefore count each overlap individually ?
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