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When you retrieve the differentially bound sites with dba.report(), there is a "Conc" column that shows the mean read concentration over all the samples (log2 normalized ChIP read counts with control read counts subtracted). Is there a way to calculate those numbers for arbitrary regions (not just differentially bound)?
Yes, I know, but those are the regions as determined by DiffBind. My question is if I want to look at arbitrary regions. For example, regions that were found in a different experiment.
Hi,
You can't probe arbitrary regions on the fly. If you have a fixed list of regions, you can provide that when you count reads via the "
peaks" option, as inwhere
peaksis aGRangesor other form of peak list (see the docs for details), then it will count and calculate everything on exactly those peaks.Cheers
- Gord