Hi,

I cannot find the way to get the coordination for the summits of my peaks.

I added the summit option to the dba.count and I am looking at the dba.peakset documentation and cannot figure out how to get the data..

Is there a way to get the summits of the peaks together with the differential affinity data when using dba.report?

Thanks

You can get the summit coordinates for the full binding matrix by setting the score to DBA_SCORE_SUMMIT_POS. Here's how to do it using the example dataset:

data(tamoxifen_analysis)
tamoxifen <- dba.count(tamoxifen, peaks=NULL, score=DBA_SCORE_SUMMIT_POS)
summitCoordinates <- dba.peakset(tamoxifen, bRetrieve=TRUE)

If you want the summits for the differentially bound sites only, here's a snippet that will accomplish that:

DBreport <- dba.report(tamoxifen)
DBsites <- as.integer(names(DBreport))
summitCoordinates[DBsites,]