[BioC] downloading a conservation track with rtracklayer on several chromosome seqs
Robert Castelo
robert.castelo at upf.edu
Fri Jul 3 14:34:57 CEST 2009
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(27102150,52710874,32265941),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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