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

[Zhu, Lihua (Julie)]

Holly,

Thanks for the link! The BDPs in ChIPpeakAnno is defined purely according to
the coordinates of known genes.

Best regards,

Julie


On 12/10/12 1:30 PM, "Holly" <xyang2 at uchicago.edu> wrote:

> Julie,
> 
> A basic question to verify your definition of the bi-directional promoters is,
> did you define them purely according to the coordinates of known genes, or,
> have you referred to the experimental data, e.g. EST experiments done by
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853124/ ?
> 
> I learned a lot from the discussion with you. Thanks again,
> 
> 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
>