Hi,
I have error said
Error in if (sum(res$peaks[1]$Score < 0) > 0) { :
missing value where TRUE/FALSE needed
In addition: There were 17 warnings (use warnings() to see them)

here is my sample file

here are my peaks

I think it can find my peaks, then what's wrong with it?
r
diffbind
I would suggest you write the full path to your files.
Thank you! I've tried full path, also from this test I think the program can find my file.
So I think it may not be the file path problem. Something wrong with my broadPeak.bed file?
In addition to the full paths suggestion, I've seen similar errors when a peaks file contains no actual peaks, so I'd ensure those files actually have peaks.
Yes you are right! Thank you very much! I've already solved my problem!
so why didn't you post your solution then?