[BioC] DiffBind annotation
Rory.Stark at cruk.cam.ac.uk
Fri Sep 12 16:20:19 CEST 2014
We avoided adding annotation to DiffBind because of the other packages
that specialize in this. They don't take a DiffBind object directly, but
you can always retrieve any peak set as a GRanges object, which is
commonly used in Bioconductor packages. The main packages I use for
annotation and gene set enrichment are ChIPpeakAnno and chipenrich.
Peaksets are returned as GRanges objects by default by dba.peakset() (with
bRetrieve=TRUE), dba.report() (for differentially bound peaks), and
dba.overlap() (for peaks that do or don't overlap between peak sets; you
can also use dbaPlotVenn() with bReturnPeaksets=TRUE).
On 11/09/2014 21:22, "Dolgalev, Igor" <Igor.Dolgalev at nyumc.org> wrote:
>I am getting started with DiffBind. I am really enjoying all the options
>it provides. Unfortunately, it does not seem to do any annotation. For
>example, it would be great to get the closest gene or distance to TSS/TTS
>for the binding sites. I know there are tools available for this purpose.
>Is there a specific one that you would recommend and that would integrate
>with DiffBind (if it could take DBA object directly, for example)?
>Any assistance would be much appreciated.
>Thank you very much.
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