On Sat, Dec 25, 2010 at 8:36 AM, Ann Loraine <aloraine@gmail.com> wrote:

> Hello,
>
> I have a quick question about how this is working behind the scenes.
>
> Does the code access the Table Browser web interface at UCSC?
>
> I'm very interested in this .. it seems like a very convenient way to
> access a lot of data in various useful formats without having to
> manually download anything.
>
>
The rtracklayer package does the actual data access, and yes it's through
the table browser. You can download any table you want through the low-level
rtracklayer interface.


> Is there an easy way I can browse the source code on-line or check out
> just a portion of the Bioconductor repository so that I can see how
> this feature is working?
>
> Where does this code reside in the repository?
>
> (I'm looking at http://www.bioconductor.org/developers/source-control/)
>
> Sincerely,
>
> Ann Loraine
>
>
>
> On Thu, Dec 23, 2010 at 11:18 PM, Vincent Carey
> <stvjc@channing.harvard.edu> wrote:
> > I just ran the code successfully with sessionInfo below.  Could be
> transient
> > network issue?
> >
> >> sessionInfo()
> > R version 2.12.0 Patched (2010-11-28 r53696)
> > Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit)
> >
> > locale:
> > [1] C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices datasets  tools     utils     methods
> > [8] base
> >
> > other attached packages:
> > [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2   IRanges_1.8.7
> > [4] weaver_1.16.0         codetools_0.2-6       digest_0.4.2
> >
> > loaded via a namespace (and not attached):
> > [1] BSgenome_1.18.2    Biobase_2.10.0     Biostrings_2.18.2
> > DBI_0.2-5
> > [5] RCurl_1.5-0        RSQLite_0.9-4      XML_3.2-0
> > biomaRt_2.6.0
> > [9] rtracklayer_1.10.6
> >
> >
> > On Thu, Dec 23, 2010 at 8:52 PM, Burak Kutlu <bkutlu@systemsbiology.org
> >wrote:
> >
> >> D'oh!
> >>
> >> Here it is
> >>
> >> > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =
> >> "knownGene")
> >> Download the knownGene table ... Error in curlPerform(url = url,
> >> headerfunction = header$update, curl = curl,  :
> >>  transfer closed with outstanding read data remaining
> >>
> >> I also failed to mention this is about GenomicFeatures package.
> >> Thanks Steve!
> >> -burak
> >>
> >> On Thu, Dec 23, 2010 at 4:46 PM, Steve Lianoglou
> >> <mailinglist.honeypot@gmail.com> wrote:
> >> > Hi,
> >> >
> >> > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu <
> bkutlu@systemsbiology.org>
> >> wrote:
> >> >> Hi
> >> >>
> >> >> For some reason I started getting error for the following call
> >> >> hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename
> =
> >> >> "knownGene")
> >> >
> >> > I'm not sure how we can shed some light on this without you providing
> >> > the error that you're getting ;-)
> >> >
> >> > Can you paste that into a follow up email?
> >> >
> >> > Thanks,
> >> >
> >> > -steve
> >> >
> >> > --
> >> > Steve Lianoglou
> >> > Graduate Student: Computational Systems Biology
> >> >  | Memorial Sloan-Kettering Cancer Center
> >> >  | Weill Medical College of Cornell University
> >> > Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
> <http://cbio.mskcc.org/%7Elianos/contact>
> >> >
> >>
> >>
> >>
> >> --
> >> Burak Kutlu, PhD.
> >> Research Scientist
> >> Hood Lab
> >> Institute for Systems Biology
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

