Stefan, Thanks to you and Jianhong, the assignChromosomeRegion function now has two additional parameters, one is NucleotideLevel (TRUE or FALSE) to allow both peak centric and nucleotide centric view, and the other is precedence, which specifies the precedence of the regions. If no precedence specified, double count will be enabled, which means that if a peak overlap with both promoter and 5'UTR, then both promoter and 5'UTR will be incremented. If a precedence order is specified, for example, if promoter is specified before 5'UTR, then only promoter will be incremented for the same example. In addition, Jaccard index is computed. Please let us know if you find anything unusual. Many thanks for sharing your insights with us! Best regards, Julie