[BioC] rtracklayer: Problems running vignette
anders at ebi.ac.uk
Wed Jun 3 12:22:55 CEST 2009
I've just tried to use rtracklayer, following your vignette, and ran
into two problems.
1. I cannot add any tracks to a session.
I entered the code in the vignette to produce the "targets" track and
exported it as "targets.bed". To make things easier to follow, let's
say, I start from there with a fresh R session:
# Import the data
targets <- import("targets.bed")
# targets is now a RangedData object with 3052 ranges and
# sequence names chr1 chr10 chr11 chr12 ...
# Create a session
session <- browserSession("UCSC")
# Add the 'targets' track to the session:
track(session, "MYTRACK") <- targets
Is this last command correct? It does not produce an error, but it does
not seem to do anything, either. If I list all the tracks in the session
I get a list of 196 UCSC standard tracks, but "MYTRACK" is not mentioned.
How do I correctly add a track?
2. There is some mangling happening with the chromosome names.
The man page for 'browserView' suggests to try:
browserView(session, GenomicRanges(20000, 50000, "chr2"))
Doing this asks my web browser to open the following URL:
Note that it says "chrchr2", i.e., a superfluous "chr" got prefixed to
the sequence name. Obviously, the UCSC page cannot deal with this and
I run into the same problem if I follow the vignette's code to
If I try
browserView(session, GenomicRanges(20000, 50000, "2"))
I get the range chr2:20000-50000 correctly displayed in my web browser.
There is, however, still now sight of "MYTRACK".
What's going wrong here?
R version 2.9.0 (2009-04-17)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 rtracklayer_1.4.0 RCurl_0.94-1
loaded via a namespace (and not attached):
 Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0
| Dr. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| office phone +44-1223-492680, mobile phone +44-7505-841692
| preferred (permanent) e-mail: sanders at fs.tum.de
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