Hello,
I get an error :
> session <- browserSession("UCSC")
> consQuery <- ucscTableQuery(session, "Conservation",
> GRangesForUCSCGenome("hg9", "chr1", IRanges(100000000, 101000000)),
> "phyloP46wayPlacental")
> consQuery
Get table 'phyloP46wayPlacental' from track 'Conservation' within
hg19:chr1:100000000-101000000
> conservation <- track(consQuery)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
solving row 100001: range cannot be determined from the supplied arguments
(too many NAs)
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] rtracklayer_1.20.4 GenomicRanges_1.12.5 IRanges_1.18.3
[4] BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 RCurl_1.95-4.1
[5] Rsamtools_1.12.4 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1
[9] zlibbioc_1.6.0
This could be because of a limit on the size of the results from the UCSC
server. It works with a smaller width query 1000 bases wide. It could fail with
a more informative error, and provide a warning about this in the help file of
ucscTableQuery. I wish we could convince UCSC to remove these restrictions from
a time when computing power was much less.
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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