Alec, Thank you very much for your feedback and kind words! ChIPpeakAnno does not keep the score in the annotated output. However, you could use add score to the annotated data. Here is the psudo code. AnnotatedPeak = as.data.frame(annotatePeakInBatch(...)) Data.withScore = read.table(yourBedfile, sep="\t", header=FALSE) Colnames(Data.withScore)[1:5] =c("chrom", "start", "end", "name", "score") AnnotatedPeak.withScore = merge(AnnotatedPeak, Data.withScore[,1:5], by.x=c("space", "start", "end"), by.y= c("chrom", "start", "end"), all=TRUE) Hope this is what you are looking for. Best regards, Julie On 10/9/13 6:03 PM, "Alec W. Uebersohn" <alec.w.uebersohn at="" lawrence.edu=""> wrote: > Hello! > > I am currently sitting on a mountain of ChIP-seq data and I first would like > to say that ChIPpeakAnno has been of great help to me and my PI, who are > taking this project on alone, so thank you very much for you and your team's > contribution to biology and bioinformatics! I have a question regarding > ChIPpeakAnno's use of BED scores, or what is essentially the averaged ChIP > counts for our peaks. When performing the BED2RangedData function, do these > numbers carry forward into the ranged data? Is there a way to make them do > so, and also carry forward into the annotation data? I am happy with the job > this package does in annotating my peaks, but I also would like the final > table of data to contain the BED score/ChIP counts for each annotated peak so > that I can rank genes by their level of enrichment in our ChIP-seq experiment. > Is there a way for ChIPpeakAnno to do this? My only other idea was to > annotate with, for example, the select="first" argument to obtain a list of > single annotations for each peak (so each peak appears only once in the > annotation table) and then sort that table in the same way my BED file is > sorted so that I can copy and paste the BED file's "score" column into the > annotation table and then assume that it aligned properly. > > Thank you so much for any help or advice you can offer! > > > Alec W. Uebersohn > Research Technician, Dickson Lab > Lawrence University '13 > Cell: (262) 443-4949