GRanges intersect and setdiff doesn't add up

Question

[chualec]

Hi, I'm comparing two datasets using GRanges to see how many peaks are retained or leave after a certain treatment. However, when I do the code, it doesn't quite add up. I have 2 datasets called "untreated" and "treated"

peaks_stay <- intersect(untreated, treated)
peaks_leave <- setdiff(untreated, treated)

length(peaks_stay)
16850

length(peaks_leave)
66873

length(untreated)
50883

I am not quite sure why there are more peaks identified using setdiff compared to the original. Can anyone help me with this?

Thanks in advance!

[Prakash]

What is total number of genomic regions in treated here?