[BioC] Use ChIPpeakAnno to find two-sided nearest genes to a peak

[Zhu, Lihua (Julie)]

Dear Holly,

I believe that you are interested in finding the peaks that reside in
bi-directional promoters. If so, you can use the following functions in
ChIPpeakAnno.

BDP = peaksNearBDP(peaks, AnnotationData=TSS, MaxDistance =5000)
c(BDP$percentPeaksWithBDP, BDP$n.peaksWithBDP, BDP$n.peaks)
all.genes = union(annotated.peaks$feature, BDP$peaksWithBDP$feature)
where annotated.peaks is generated from annotatePeakInBatch using TSS. To
learn more about peaksNearBDP, please type ?peaksNearBDP in R.

If you just want to find genes on both side of the peaks within certain
distance away from the peaks, you can use the following command.

Annotated.peaks = annotatePeakInBatch(peaks, AnnotationData = TSS,
output="both",select="all", maxgap=1000000)
Where maxgap can be adjusted according to your needs.

Please let me know if this suits your needs. Thanks!

Best regards,

Julie



On 12/10/12 11:19 AM, "Holly" <xyang2 at uchicago.edu> wrote:

> Dear Lihua,
> 
> I am trying to annotate peaks for not only the genes with the nearest
> TSS but the ones at the other side of the peaks.
> Do you think I can use ChIPpeakAnno to get both sided genes for a peak
> region? If so, what do you suggest?
> Thanks a lot,
> 
> Holly