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

[Holly]

Julie,

You are much helpful. Thanks!
I will forward it to people who have similar question.

Holly



On 12/10/2012 10:46 AM, Zhu, Lihua (Julie) wrote:
> 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