[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"))


# above command return NULL, it shouldn't be the correct result!


#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)

R version 2.10.0 Under development (unstable) (2009-07-06 r48901) 

[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