Dear Carl, Yes, you can use ChIPpeakAnno::annotatePeakInBatch to determine the distance from each DM site to the nearest gene - as measured from the DM site to the nearest end of the gene by setting the parameter FeatureLocForDistance = 'geneEnd'. Do you mind sharing your insight about using gene end instead of TSS? Thanks! Best regards, Julie On 5/17/12 2:43 AM, "Carl Baribault" <cbaribau at="" tulane.edu=""> wrote: > Dear Dr. Zhu, > > First, thank you and your colleagues for all your efforts in > developing the subject R package. > > I have two bed files containing > significantly-differentially-methylated- (or DM) sites and genes, > respectively. > > I'd like to know if the subject method, > ChIPpeakAnno::annotatePeakInBatch, can be used to determine the > distance from each DM site to the nearest gene - as measured from the > DM site to the nearest end of the gene, rather than the TSS of the > gene. > > Best, > Carl Baribault > Tulane Cancer Center