Dear Pablo, If you type ?annotatePeakInBatch in a R session after library(ChIPpeakAnno), you will notice that you can annotate your peaks with your own annotation or built-in annotation dataset. The following are a few built-in annotation datasets. data(TSS.human.NCBI36),data(TSS.mouse.NCBIM37), data(GO.rat.RGSC3.4) and data(TSS.zebrafish.Zv8). You probably already notice that the main ID of the built-in dataset is Ensembl_ID. You could use getBM function in biomaRt package to convert ensembl_ID to gene name or other IDs if needed. Best regards, Julie On 1/19/11 2:10 PM, "Pablo Echeverria" <pablo.echeverria at="" unige.ch=""> wrote: > Dear Julie, > > I'm starting using ChIPpeakAnno. > I'm analyzing chip-seq data, comparing datasets from my lab and other > and I mainly would like to obtain from the bed files that I'm using, > some of the features that are described in your paper (those are already > working), but also I need to retrieve gene names associated to my peaks. > > How can I get, and excel file with the associated gene name to the > enriched peaks. > Could you give the lines that I have to write to get those tables? > > Thank you in advance, > > Pablo >