Entering edit mode
Hi,
I wanted to try out UCSC views in rtracklayer but I seem to have
fallen at
the first hurdle. I could not get the example code for browserView()
to
work and it throws an error I don't understand. Session info below.
Looks like I'm the second person to report this problem this year (no
reply
to the first)
https://stat.ethz.ch/pipermail/bioconductor/2014-April/058989.html
Dave Gerrard
> require(rtracklayer)
> session <- browserSession()
> browserView(session,
+ GRangesForUCSCGenome("hg19", "chr2", IRanges(20000,
50000)))
Warning message:
In .local(object, range, track, ...) : NAs introduced by coercion
Error in ucscTrackModes(ucscTracks(object)) :
error in evaluating the argument 'object' in selecting a method for
function 'ucscTrackModes': Error in names(trackIds) <- sub("^ ", "",
sapply(nodes, xmlValue)) :
attempt to set an attribute on NULL
>
> traceback()
7: ucscTrackModes(ucscTracks(object))
6: .local(object, ...)
5: ucscTrackModes(view)
4: ucscTrackModes(view)
3: .local(object, range, track, ...)
2: browserView(session, GRangesForUCSCGenome("hg19", "chr2",
IRanges(20000,
50000)))
1: browserView(session, GRangesForUCSCGenome("hg19", "chr2",
IRanges(20000,
50000)))
> sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
base
other attached packages:
[1] rtracklayer_1.22.5 GenomicRanges_1.14.4 XVector_0.2.0
IRanges_1.20.7 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] Biostrings_2.30.1 bitops_1.0-6 BSgenome_1.30.0
RCurl_1.95-4.1
Rsamtools_1.14.3
[6] stats4_3.0.3 tools_3.0.3 XML_3.98-1.1
zlibbioc_1.8.0
>
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