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 [[alternative HTML version deleted]]