I want to retrieve the gene names for multiple genomic ranges using rtracklayer. This is what I tried: library("rtracklayer") session <- browserSession("UCSC") genome(session) <- "hg17" gr1 = GenomicRanges(start=26970000, end=26980000, chr=7, genome="hg17") gr2 = GenomicRanges(start=156295000, end=156305000, chr=7, genome="hg17") gr3 = GenomicRanges(start=c(26970000, 156295000), end=c(26980000, 156305000), chr=c(7, 7), genome="hg17") gr4 = GenomicRanges(start=c(156295000, 26970000), end=c(156305000, 26980000), chr=c(7, 7), genome="hg17") tq = ucscTableQuery(session, track="knownGene", table="knownGene", range=gr1) getTable(tq) For gr1 and gr2 the result is as expected, the genes HXA9 and HLXB9, but for gr3 and gr4 only the first one (by genomic position) is returned. Is this kind of query possible with rtracklayer in general? > sessionInfo() R version 2.10.0 RC (2009-10-18 r50160) x86_64-pc-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.6.0 RCurl_1.3-1 bitops_1.0-4.1 affy_1.24.2 [5] Biobase_2.6.1 loaded via a namespace (and not attached): [1] BSgenome_1.14.2 Biostrings_2.14.10 IRanges_1.4.9 [4] XML_2.6-0 affyio_1.14.0 preprocessCore_1.8.0 [7] tools_2.10.0 Thanks in advance, Christian

On Tue, Feb 9, 2010 at 7:35 AM, Christian Ruckert <cruckert@uni-muenster.de>wrote: > I want to retrieve the gene names for multiple genomic ranges using > rtracklayer. This is what I tried: > > library("rtracklayer") > session <- browserSession("UCSC") > genome(session) <- "hg17" > > gr1 = GenomicRanges(start=26970000, end=26980000, chr=7, genome="hg17") > > gr2 = GenomicRanges(start=156295000, end=156305000, chr=7, genome="hg17") > > gr3 = GenomicRanges(start=c(26970000, 156295000), end=c(26980000, > 156305000), chr=c(7, 7), genome="hg17") > > gr4 = GenomicRanges(start=c(156295000, 26970000), end=c(156305000, > 26980000), chr=c(7, 7), genome="hg17") > > tq = ucscTableQuery(session, track="knownGene", table="knownGene", > range=gr1) > getTable(tq) > > > For gr1 and gr2 the result is as expected, the genes HXA9 and HLXB9, but > for gr3 and gr4 only the first one (by genomic position) is returned. Is > this kind of query possible with rtracklayer in general? > > > No, but it's on the TODO list. Still reverse engineering that table browser. Btw, if all you need are the UCSC genes, try the GenomicFeatures suite of packages. Sorry, Michael > > sessionInfo() > R version 2.10.0 RC (2009-10-18 r50160) > x86_64-pc-linux-gnu > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.6.0 RCurl_1.3-1 bitops_1.0-4.1 affy_1.24.2 > [5] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] BSgenome_1.14.2 Biostrings_2.14.10 IRanges_1.4.9 > [4] XML_2.6-0 affyio_1.14.0 preprocessCore_1.8.0 > [7] tools_2.10.0 > > > Thanks in advance, > Christian > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]