Hi Alejandra- You're pretty much figured it out. After running dba.count() and having it derive a merged peakset, the $sites element is a list with one logical vector per sample. These vectors are all the same length as the number of peaks in the merged set. The logical values indicate if the merged peak overlapped with a peak in the original peakset, and is used internally to support the bCalled and bCalledDetail options in dba.report(). Site vectors are also accepted as parameters to dba.plotHeatmap() and dba.plotPCA() to identify a subset of global sites (e.g. only the sites identified in one of the original peaksets). Cheers- Rory From: Alejandra Eugenia Medina Rivera <medina.alexiel@gmail.com<mailto:medina.alexiel@gmail.com>> Date: Fri, 13 Jun 2014 16:32:10 -0400 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind, dba.count result object Hi I have a question about the content of the dba.count result object. There is "sites" element that is logical, and I would like to know what it contains. Is it indicating if a peak is a peak in each data set? Thanks Alejandra >names(dba.count.object$sites) [1] "HEPG2_1" "HUVEC_1" "HeLaS3_1" [4] "K562_1" "HaoEC_1" "HEPG2_2" >head(dba.count.object$sites[[1]]) [1] FALSE FALSE FALSE FALSE FALSE FALSE....... Cheers Alejandra -- Alejandra Eugenia Medina Rivera. SickKids [[alternative HTML version deleted]]