Sorry for replying so late. I have been out of email contact.

On Tue, Jul 7, 2009 at 12:05 AM, LiGang <luzifer.li@gmail.com> wrote:

> #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!
>


For me, this returns:
[1] "phastCons30wayPlacental" "phastCons30wayEuarch"
[3] "phastCons30way"          "multiz30waySummary"
[5] "multiz30wayFrames"       "multiz30way"

R version 2.10.0 Under development (unstable) (--)
i686-pc-linux-gnu

locale:
[1] C

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    IRanges_1.3.34

loaded via a namespace (and not attached):
[1] BSgenome_1.13.6   Biobase_2.3.11    Biostrings_2.13.9 XML_2.5-3



> 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
> #==================
>
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