Dear experts, Given the accession IDs such as these: How can I extract the "chromosome name", "start" and "end" position of each ID, with BioConductor. AB002292 AB002296 AB002298 AB002303 .. EF565109 K03493 L36149 M16404 X80391 Z25470 I tried this, but it gives me so many coordinates sets instead of just 3 (corresponding to query). > library(biomaRt) > acc <- c("AB002292", "X80391", "Z25470") > mart <- useMart("ensembl") > mart <-useDataset("hsapiens_gene_ensembl",mart) > t <- getBM(attributes=c("chromosome_name", "start_position", "end_position"), values=acc, mart=mart) > t Please kindly advice. - Gundala Viswanath Jakarta - Indonesia

On Fri, Oct 3, 2008 at 3:29 AM, Gundala Viswanath <gundalav at="" gmail.com=""> wrote: > Dear experts, > > Given the accession IDs such as these: > > How can I extract the "chromosome name", "start" and "end" position > of each ID, with BioConductor. > > AB002292 > AB002296 > AB002298 > AB002303 > .. > EF565109 > K03493 > L36149 > M16404 > X80391 > Z25470 > > I tried this, but it gives me so many coordinates sets instead of just > 3 (corresponding > to query). > >> library(biomaRt) >> acc <- c("AB002292", "X80391", "Z25470") >> mart <- useMart("ensembl") >> mart <-useDataset("hsapiens_gene_ensembl",mart) >> t <- getBM(attributes=c("chromosome_name", "start_position", "end_position"), values=acc, mart=mart) Close. You simply need to specify a filter on embl id. t <- getBM(attributes=c("chromosome_name", "start_position", "end_position",'embl'), filters=c('embl'), values=acc, mart=mart) I added a column in the output to show the embl id, also. Sean

Hi Gundala, Gundala Viswanath wrote: > Dear experts, > > Given the accession IDs such as these: > > How can I extract the "chromosome name", "start" and "end" position > of each ID, with BioConductor. > > AB002292 > AB002296 > AB002298 > AB002303 > .. > EF565109 > K03493 > L36149 > M16404 > X80391 > Z25470 > > I tried this, but it gives me so many coordinates sets instead of just > 3 (corresponding > to query). > >> library(biomaRt) >> acc <- c("AB002292", "X80391", "Z25470") >> mart <- useMart("ensembl") >> mart <-useDataset("hsapiens_gene_ensembl",mart) >> t <- getBM(attributes=c("chromosome_name", "start_position", "end_position"), values=acc, mart=mart) You need a filter argument as well. In addition, I usually like to put the input argument into the attributes as well, so you can line things up if there are certain IDs that don't return a result. > getBM( c("embl","chromosome_name","start_position","end_position"),"embl", acc, mart) embl chromosome_name start_position end_position 1 AB002292 8 1759549 1894206 2 X80391 17 3141679 3142644 3 Z25470 18 13815543 13816861 In this case it isn't necessary, but it might be for your whole vector of IDs. Best, Jim >> t > > Please kindly advice. > > > - Gundala Viswanath > Jakarta - Indonesia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662