Dear list, Is there a way to keep track of the values used for the filter when using the getBM() function from the biomaRt package? I have some genomic regions and want to find out what genes are in these regions. This is simple enough using getBM(): require(biomaRt) ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") # For these Genomic regions: regs <- c("10:66817823:68817823", "10:118963569:120963569", "4:156786028:158786028") # Get all genes in these regions and their start/end positions genesInRegion <- getBM(mart=ensembl, filters="chromosomal_region", value=regs, attr=c("ensembl_gene_id", "start_position", "end_position")) This results in a table of gene ids and the genomic locations of these genes. However, we lose data on what genes map to which of the original regions that were used for the search. I could work this out as a further step, using e.g. GenomicRanges, but I wonder if there is simpler way, i.e. a way to keep track of the original values used for the getBM function call, and perhaps a way to return them as part of the getBM results along with the gene information. I could just go through each genomic location in the regs vector, but this would take a long time for long lists of regions (the examples included here are just for illustrative purposes, in reality I will have a large list of smaller regions). There was talk about producing a wrapper, quite a few years ago now, but I don't know if this happened: https://stat.ethz.ch/pipermail/bioconductor/2009-November/030656.html Any help/tips would be most appreciated, Many thanks for your time, Jim -- James R Perkins, PhD [[alternative HTML version deleted]]