Joanne,

Given a peak dataset peaks in RangedData and an annotation dataset miRNAs you obtained from getAnnotation, then you can use the following code to obtain the nearest miRNAs.

nearest.miRNAs = as.data.frame(annotatePeakInBatch(peaks, AnnotationData = miRNAs))

Please type ?annotatePeakInBatch in R to view other examples.

You can also access the documentation at http://www.bioconductor.org/packages/2.10/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf, and the publication at http://www.biomedcentral.com/1471-2105/11/237/.

Best regards,

Julie

On 8/30/12 4:02 PM, "Ngeow, Joanne" <ngeowj@ccf.org> wrote:

Dear Julie,

Thank your for your response but I am unclear as to what you mean by that- do you have a sample of the code to use to

  1.  get ensembl data for miRNA
  2.  correlate with my peaks
  3.  identify which miRNAs are the ones called out

I am sorry but I am very new to ChIPpeakAnno as you can tell. For TSS, it is easier to find solutions on line but I can’t seem to find what I need on miRNAs

Thank you, your help is much appreciated
Joanne

On 8/29/12 6:04 PM, "Zhu, Lihua (Julie)" <Julie.Zhu@umassmed.edu> wrote:

Joanne and Dingxia,

You need to call annotatePeakInBatch with your peaks and the Annotation you obtained. By calling data(annotatedPeak), you are running the examples in the ChIPpeakAnno package.

Best regards,

Julie


From: "Ngeow, Joanne" <ngeowj@ccf.org>
Date: Wed, 29 Aug 2012 16:17:21 -0400
To: Lihua Julie Zhu <julie.zhu@umassmed.edu>
Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
Subject: Re: RE ChIPPEAKANNO

Dear Julie,

Thanks. I’ve attached it in the files. The output I got is shown but I would like to identify what the peaks are and I am struggling with that as well as am not sure if I am extracting the info correctly from ensembl for miRNA

Thank you
Joanne


On 8/27/12 6:25 PM, "Zhu, Lihua (Julie)" <Julie.Zhu@umassmed.edu> wrote:

Joanne,

Could you please send us the code snippet and session info? Thanks!

Best regards,

Julie


On 8/27/12 4:00 PM, "Ngeow, Joanne" <ngeowj@ccf.org> wrote:

Hi Julie,
I was using ChIPPeakAnno and was able to extract the distance to nearest miRNA which is what I am interested in. I am having trouble however going from that step to finding out which are the miRNAs that is being mapped.Can’t find the answer online/ blogs.  Can you help?

Thank you

Best regards
Joanne Ngeow
Cancer Genetics Fellow

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