exomePeak for non-fragmented libraries

Hi,

I came across this tool:
bioconductor.riken.jp/packages/3.7/bioc/manuals/exomePeak/man/exomePeak.pdf

I have non-fragmented libraries (meaning the RNA was not fragmented before sequencing). This means many tools like macs2 etc cannot be used. But can I use exomePeak?
I went over the manual, and it seems to expect fragmented data, but I was not sure...

Thanks for your input,