upstream <- flank(myPeakList, 10000)
downstream <- flank(myPeakList, 50000, FALSE)
upstream.genes <- subsetByOverlaps(tx.ranges, upstream)
downstream.genes <- subsetByOverlaps(tx.ranges, downstream)


On Thu, May 17, 2012 at 1:17 PM, Yadav Sapkota <ysapkota@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@umassmed.edu
> > wrote:
>
> > Yadav,
> >
> > You could try annotatePeakInBatch in ChIPpeakAnno package.
> >
> > Best regards,
> >
> > Julie
> >
> >
> > On 5/17/12 12:40 PM, "Yadav Sapkota" <ysapkota@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]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
> >
>
>
> --
> Yadav Sapkota
> PhD Candidate
> Dept. of Laboratory Medicine and Pathology, UofA
> Cross Cancer Institute
> 11560 University Avenue, Edmonton AB T6G 1Z2
> Phone: 780-5778092
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
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> Search the archives:
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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