I am sure this is been dealt before by Chip Seq experts... I was wondering what methods, preferably in R, are available to plot the distribution of the heights of Chip Seq peaks mapped on the genome. I see that there are several packages such as ChIPseeker and deepTools that will plot either heat maps or frequencies weighted by the height of the peaks, I guess this is done because reads are not uniformly distributed across the genome but why not plot directly the mean distribution of heights normalised by the total number of peaks in a histogram for example? What are the issues here that I am not seeing?
Thank you very much for your insight