Entering edit mode
Li, Xuejun
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10
@li-xuejun-4057
Last seen 10.1 years ago
Hello everything,
I have a question regarding the getTable function in the rtracklayer
package. The code below used to work in previous R version, but it
doesn't for the current release. I can't figure out what the problem
is.
Can anyone give some hint? Thanks for your help!
Best,
Arthur Xuejun Li
City of Hope Comprehensive Cancer Center
Department of Information Science
1500 East Duarte Road
Duarte, CA 91010 - 3000
Ph: (626) 256-4673 ext. 65121
Fax: (626) 471-7106
> session <- browserSession()
> genome(session) <- "mm9"
> foo <- trackNames(session)[trackNames(session) =="rmsk"]
> bar<- ucscTableQuery(session, foo)
> bar1 <- getTable(bar)
Error in if (st[["status"]] == 100) { :
missing value where TRUE/FALSE needed
>
>
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.8.1 RCurl_1.4-1 bitops_1.0-4.1
[4] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5
[7] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 BSgenome_1.16.0 grid_2.11.0 hwriter_1.2
[5] tools_2.11.0 XML_2.8-1
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