downloading a conservation track with rtracklayer on several chromosome seqs
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Robert Castelo ★ 2.9k
@rcastelo
Last seen 18 days ago
Barcelona/Universitat Pompeu Fabra
dear list, i'd like to know how can i download the conservation track for several genomic ranges belonging to different chromosome sequences as the example below seems only to retrieve this information for 1 of the chromosomes, (the first one on the list): library(rtracklayer) session <- browserSession("UCSC") genome(session) <- "hg18" track(session, "Conservation", GenomicRanges(start=c(27099139,52708461,32260488),end=c(27102150,52710 874,32265941),chrom=c("chr7","chr12","chr6"), genome="hg18")) UCSC track 'Primate Cons' UCSCData: 3012 ranges by 1 columns columns(1): score sequences(1): chr7 thanks! robert. sessionInfo() R version 2.9.1 (2009-06-26) x86_64-unknown-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] BSgenome_1.12.2 Biobase_2.4.1 Biostrings_2.12.7 IRanges_1.2.3 [5] XML_2.5-3
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@michael-lawrence-2759
Last seen 8.0 years ago
On Fri, Jul 3, 2009 at 5:34 AM, Robert Castelo <robert.castelo@upf.edu>wrote: > dear list, > > i'd like to know how can i download the conservation track for several > genomic ranges belonging to different chromosome sequences This is not supported yet, mostly because whenever people have multiple regions, they have a lot of regions, and the current, simple implementation would be too slow. It is possible though to upload a track to UCSC and ask it for the regions that intersect that track. I'll put that on the TODO list; actually it was already on there. For now, you might just have to loop in R and make separate requests. > as the > example below seems only to retrieve this information for 1 of the > chromosomes, (the first one on the list): > > library(rtracklayer) > > session <- browserSession("UCSC") > > genome(session) <- "hg18" > > track(session, "Conservation", > GenomicRanges(start=c(27099139,52708461,32260488),end=c(27102150,527 10874,32265941),chrom=c("chr7","chr12","chr6"), > genome="hg18")) > UCSC track 'Primate Cons' > UCSCData: 3012 ranges by 1 columns > columns(1): score > sequences(1): chr7 > > thanks! > robert. > > sessionInfo() > R version 2.9.1 (2009-06-26) > x86_64-unknown-linux-gnu > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] BSgenome_1.12.2 Biobase_2.4.1 Biostrings_2.12.7 > IRanges_1.2.3 > [5] XML_2.5-3 > > _______________________________________________ > 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]]
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