Entering edit mode
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(âyourPeakfileâ, sep=â\tâ,
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 filesãI 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.
[[alternative HTML version deleted]]