[Bioc-sig-seq] annotatePeakInBatch feature request

[Dario Strbenac]

Hi,

My idea was that if you did a ChIP for a transcription factor, the peaks would be strand specific. If your peak and gene were on the + strand, the current method gives you the distance from the left edge of the peak to the left edge of the gene, but say if the gene and peak are both on the negative strand, the current method gives you the distance from the right edge of the gene, to the left edge of the peak.

i.e. + strand

5'|peak|-------|gene|------------------3'
3'|--distance--|------------------5'

    - strand

5'--------------------------------------3'
3'--|gene|----------------|peak|--------5'
         |------distance--|

So, it'd be good to have the same style of distance for negative strand peaks

e.g.

5'--------------------------------------3'
3'--|gene|----------------|peak|--------5'
         |------distance-------|

No rush. Just a suggestion.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia


---- Original message ----
>Date: Fri, 4 Jun 2010 11:11:28 -0400
>From: "Zhu, Julie" <Julie.Zhu at umassmed.edu>  
>Subject: Re: [Bioc-sig-seq] annotatePeakInBatch feature request  
>To: "D.Strbenac at garvan.org.au" <D.Strbenac at garvan.org.au>, "bioc-sig-sequencing at r-project.org" <bioc-sig-sequencing at r-project.org>
>
>Hi Dario,
>
>If possible, could you please share your insight on the use case for
>distinguishing peaks at + strand from those at - strand? Thanks!
>
>I have several deadlines coming next week. I will try to work on the new
>feature the week after. Thanks!
>
>Best regards,
>
>Julie
>
>
>*******************************************
>Lihua Julie Zhu, Ph.D
>Research Associate Professor
>Program in Gene Function and Expression
>Program in Molecular Medicine
>University of Massachusetts Medical School
>364 Plantation Street, Room 613
>Worcester, MA 01605
>508-856-5256
>http://www.umassmed.edu/pgfe/faculty/zhu.cfm
>
>
>
>On 6/3/10 11:26 PM, "Dario Strbenac" <D.Strbenac at garvan.org.au> wrote:
>
>> Hi,
>> 
>> Would it be possible to have an extra choice for the PeakLocForDistance option
>> of the annotatePeakInBatch function ? A choice that uses the start if the peak
>> is on the + strand, and end if the peak is on the - strand (if the peaks have
>> a strand) ?
>> 
>> --------------------------------------
>> Dario Strbenac
>> Research Assistant
>> Cancer Epigenetics
>> Garvan Institute of Medical Research
>> Darlinghurst NSW 2010
>> Australia
>> 
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>> 
>
>