[BioC] Query neighboring genes

[Zhu, Lihua (Julie)]

Yadav,

Please set parameters output = "both", maxgap = 100000, select="all"
followed by filtering the results further using a combination of
insideFeature and shortestDistance. For detailed parameter setting, please
type help(annotatePeakInBatch) in a R session.

For example, the following will return peaks located within 5kb downstream
of a gene.

 annotatedPeak[!is.na(annotatedPeak$insideFeature) &
annotatedPeak$insideFeature == "downstream" &
!is.na(annotatedPeak$shortestDistance) & annotatedPeak$shortestDistance
<=5000,]

Best regards,

Julie


On 5/17/12 4:17 PM, "Yadav Sapkota" <ysapkota at ualberta.ca> wrote:

> Hi,
> 
> I tried this function and it works fine for me however, I could not find any
> option to define the upstream and downstream size while looking for
> neighboring genes.
> 
> For example, I wanted to only query genes that are located 100 KB upstream and
> 50 KB downstream from a chromosomal range. Any hint would be appreciated.
> Below is the code I am using for demo:
> 
> source("http://bioconductor.org/biocLite.R")
> biocLite("ChIPpeakAnno")
> library("ChIPpeakAnno")
> data(myPeakList)
> data(TSS.human.GRCh37)
> annotatedPeak = annotatePeakInBatch (myPeakList[1:6,], AnnotationData =
> TSS.human.GRCh37)
> 
> --Yadav
> 
> 
> 
> 
> On Thu, May 17, 2012 at 10:52 AM, Zhu, Lihua (Julie) <Julie.Zhu at umassmed.edu>
> wrote:
>> Yadav,
>> 
>> You could try annotatePeakInBatch in ChIPpeakAnno package.
>> 
>> Best regards,
>> 
>> Julie
>> 
>> 
>> On 5/17/12 12:40 PM, "Yadav Sapkota" <ysapkota at ualberta.ca> wrote:
>> 
>>> Hi,
>>> 
>>> Is there any tool or package that can query neighboring genes (lets say 100
>>> KB upstream and downstream) of a specific chromosomal range (chr1:100-200)?
>>> I have thousands of these chromosomal ranges.
>>> 
>>> You help will be greatly appreciated.
>>> 
>>> Regards,
>>> Yadav Sapkota
>>> Uni of Alberta
>>> 
>>> [[alternative HTML version deleted]]
>>> 
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>> 
>> 
> 
>