Re: Query neighboring genes

Actually, for what you're doing, you want

upstream.hits <- findOverlaps(tx.ranges, upstream)
downstream.hits <- findOverlaps(tx.ranges, downstream)

interpretation as previously

On Thu, May 17, 2012 at 1:30 PM, Tim Triche, Jr. <tim.triche@...>wrote:

> 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@...>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@...
>> > wrote:
>>
>> > Yadav,
>> >
>> > You could try annotatePeakInBatch in ChIPpeakAnno package.
>> >
>> > Best regards,
>> >
>> > Julie
>> >
>> >
>> > On 5/17/12 12:40 PM, "Yadav Sapkota" <ysapkota@...> 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@...
>> > > 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]]
>>
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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>
>
>

--

-- 
*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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