Is there a way to differentiate between gain peaks and new peaks? I want to be able to get a set of peaks that exist in two sample groups, but higher in one of them and a set of peaks that only appear in one sample but not in the other (new peaks)

Thank you very much

This depends on what you mean by having the peaks "appear" in a sample.

If you mean the the peak was identified by your peak caller in a sample, then you can use the bCalled and/or bCalledDetail parameters to dba.report().

Setting bCalled=TRUE will include columns for each sample group showing the number of samples within that group where the peak was called.

Setting bCalledDetail=TRUE will include columns for each sample indicating whether the peak was called for that sample (either a + if it was called or a -if it was not).

For example:

data(tamoxifen_analysis)
tamreport <- dba.report(tamoxifen, bCalled=TRUE, bCalledDetail=TRUE)
tamreport