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 [[alternative HTML version deleted]]