[BioC] rtracklayer and multiple ranges

Christian Ruckert cruckert at uni-muenster.de
Tue Feb 9 16:35:14 CET 2010

I want to retrieve the gene names for multiple genomic ranges using 
rtracklayer. This is what I tried:

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", 

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)

[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,

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