On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders@ebi.ac.uk> wrote:

> Hi Michael,
>
> 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:
>
>  library(rtracklayer)
>
>  # 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 with
>  trackNames(session)
> I get a list of 196 UCSC standard tracks, but "MYTRACK" is not mentioned.
>
> How do I correctly add a track?
>

Well, I can say that this works for me. I need to look into parsing the
error messages returned by UCSC.  You can always try uploading to UCSC
manually to see what went wrong. I know that back in December the BED output
was mishandling the score values.


>
>
> 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:
>
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314
>
> 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 one gets
> an error message displayed by JavaScript that "chrchr2" is not known.
>
> I run into the same problem if I follow the vignette's code to demonstrate
> 'browserView'.
>
> 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?
>

Thanks for pointing this out. I've fixed this for version 1.5.3.

Michael


>
>
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.4.0 RCurl_0.94-1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.4.0     Biostrings_2.12.0 BSgenome_1.12.0   IRanges_1.2.0
> [5] XML_2.3-0
>
>
> Cheers
>  Simon
>
>
> +---
> | 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@fs.tum.de
>
>
>
>

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