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6 hours ago by

Hi,
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 :

enter image 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?

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6 hours ago
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Sam80



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