I am learning the ChIPQC package, and I fail to understand the Counts In Peaks plot (output of plotRap).
From the vignette enter link description here :
What does each data point on the boxplot stand for? According to the description, this is the number of reads that fall in a peak. If so, this means that the number of data points in the boxplot is identical to the number of reads; however then the boxplot would actually show the distribution of the pileup values.
Is that correct?