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
>
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