examples of "ucscTableQuery" in "rtracklayer" does not work
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li lilingdu ▴ 450
@li-lilingdu-1884
Last seen 4.2 years ago
#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 #==================
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@michael-lawrence-2759
Last seen 7.9 years ago
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 > #================== > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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