[BioC] question regarding ChIPPeakAnno use

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Fri Mar 16 16:33:51 CET 2012

Dear Xianyong,

You would need to use the following code without specifying the index range
for your peak. Ma[1:6,] means the first 6 peaks.

annotatedPeak = annotatePeakInBatch(ma, AnnotationData=TSS.human.NCBI36)

Hope this resolves your issue.

Best regards,


On 3/16/12 10:24 AM, "Ma, Xian-Yong" <xian-yong.ma at yale.edu> wrote:

> Hi, Dear Dr.Zhu: 
> I am Xianyong Ma from Yale Medical School, I am working on a CHIP-Sequecning
> project, and I try to use
> ChIPPeakAnno to analysis my data, it is a wonderful tool to map the binding
> sites for my purpose, now I have
> trouble when I use it, I don't understand the meaning of following sentence:
> annotatedPeak = annotatePeakInBatch(ma[1:6,],
> AnnotationData=TSS.human.NCBI36),
> when I change the [1:6] to the number [1:5000], I only got the peaks from
> chromosome 1,10 and 11, I think I should get the bindings from all chromosomes
> since I check them by another method.
> Thanks very much for your nice help!
> sincerely,
> Xianyong Ma

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