Entering edit mode
Abhishek,
Please try the following code snippets assuming your bed file is
test1.bed without header.
library(ChIPpeakAnno)
test1.bed=read.table("~/Document/test1.bed", sep="\t", skip=0,
header=FALSE)
myPeakList = BED2RangedData(test1.bed,header=FALSE)
Now you can use annotatePeakInBatch to annotate myPeakList.
For detailed information on how to use ChIPpeakAnno package, please
refer to http://www.bioconductor.org/packages/2.8/bioc/vignettes/ChIPp
eakAnno/inst/doc/ChIPpeakAnno.pdf, http://www.bioconductor.org/help
/course-materials/2010/BioC2010/BioC2010_ChIPpeakAnno.pdf
And Zhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to
annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010,
11:237doi:10.1186/1471-2105-11-237.
Best regards,
Julie
On 6/27/11 7:40 AM, "Abhishek Singh" <abhisheksinghnl@gmail.com>
wrote:
hi!
I was trying to use your R package ChIPpeakAnno to annotate my peak
files which are in .bed format.
Somehow I am unable to tell your package to load my input files and
perform analysis.
To brief you what exactly I intend to do, I have a peak file (form
MACS in .bed format) and I want to give this file as an input to your
package in R (which is already installed).
could you roughly tell me what exactly should I do so that the package
starts reading my files as an input.
Thank you for your time.
Looking forward for your reply.
Regards
Abhishek A. Singh
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