Rabe,

x = read.table(“yourfile.txt”, sep=”\t”, header=TRUE, stringsAsFactors=FALSE)
If your file does not contain a header line, set header=FALSE in the above code.
MyPeak = RangedData(IRanges(start=x[,2], end=x[,3]), names=seq(1:dim(x)[1])), space=x[,1])

Please take a look at the examples by typing help(annotatePeakInBatch) in a R session.

Best regards,

Julie


On 6/15/11 4:43 AM, "Asma rabe" <asma.rabe@gmail.com> wrote:

Hi Julie,

I would like to use ChIPpeakAnno to annotate chip-seq peaks that i've, my peaks are in tab separated file that have the coulmns below

chr start end width

I would like to put my data in IRanges in order to use ChIPpeakAnno ,can you tell me how to do that?

Thanks in advance
Best Regards,
Rabe


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