Dear Benxia,

MyPeakList is an example peak dataset. For your own analysis, you will need to read in your own peak-calling file using R data import function, e.g., yourPeak= BED2RangedData(read.table(“yourPeakfile”, sep=”\t”, header=TRUE). Then call AnnoatedPeak = annotatePeakInBatch(yourPeak, AnnotationData=TSS.human.NCBI36) assuming your data is from human.

Here is a previous post addressing your question. http://grokbase.com/t/r/bioconductor/133gezh9ap/bioc-chippeakanno
For specific parameter setting, please type help(annotatePeakInBatch) in a R session.

For detailed information, please read the paper at http://www.biomedcentral.com/1471-2105/11/237, and the user manual at http://www.bioconductor.org/packages/2.12/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf. Here is the chapter on analyzing ChIP-seq data in case you have access to the following book.
Tiling Arrays Methods in Molecular Biology Volume 1067, 2013, pp 105-124 Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset
If you want to read more, here are the presentations on previous Bioconductor meeting. FYI, the last one has FAQ section.
http://www.bioconductor.org/help/course-materials/2012/BiocEurope2012/ChIPpeakAnno-Zhu.pdf
http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/Bioc2011_ChIPpeakAnno.R
http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/ChIPpeakAnno-BioC2011.pdf

BTW, could you please copy bioconductor@r-project.org in the subsequent emails so that others can contribute/benefit? Thanks!

Best regards,

Julie





On 9/13/13 9:56 AM, "hubenxia123" <hubenxia123@163.com> wrote:

Dear professor,
     My name is  Benxia Hu,I am  a graduate student of AnHui Univesity .
  I  want to ask you  some  questions about the The ChIPpeakAnno.
 :> library(ChIPpeakAnno)
> data(myPeakList)
> data(TSS.human.NCBI36)
> annotatedPeak = annotatePeakInBatch(myPeakList[1:6,], AnnotationData=TSS.human.NCBI36)
> as.data.frame(annotatedPeak)
I don`t know what is the myPeakList  ﻿.I have analysed  the  ChIP-seq  data.so  What I have is the peak-calling files。I don`t have to do  the data(myPeakList).And my reference genome is UCSC hg19,not the  TSS.human.NCBI36.
     Thank you for  your  time.

                                                                                                                      Benxia Hu.




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