GRanges intersect and setdiff doesn't add up
0
1
Entering edit mode
2.6 years ago
chualec ▴ 20

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!

ChIP-Seq R • 441 views
ADD COMMENT
0
Entering edit mode

What is total number of genomic regions in treated here?

ADD REPLY

Login before adding your answer.

Traffic: 1224 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6