[BioC] examples of "ucscTableQuery" in "rtracklayer" does not work
LiGang
luzifer.li at gmail.com
Tue Jul 7 09:05:03 CEST 2009
#examples of "ucscTableQuery" in "rtracklayer" is shown below:
session <- browserSession()
genome(session) <- "mm9"
query <- ucscTableQuery(session, "Conservation",
GenomicRanges(57795963, 57815592, "chr12"))
tableNames(query)
# above command return NULL, it shouldn't be the correct result!
rtracklayer:::ucscTableGet(query)->out
#above command didn't retrieve the correct page
as(out, "character")->out
unlist(strsplit(out, "\n"))->out
grep("error", out, ignore.case=TRUE,value=T)
sessionInfo()
#==================
R version 2.10.0 Under development (unstable) (2009-07-06 r48901)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.5.6 RCurl_0.98-1 bitops_1.0-4.1
loaded via a namespace (and not attached):
[1] Biobase_2.5.4 Biostrings_2.13.23 BSgenome_1.13.8 IRanges_1.3.30
tools_2.10.0 XML_2.5-1
#==================
More information about the Bioconductor
mailing list