[Bioc-devel] Experimental data package or ExperimentHub
michaelisaiahlove at gmail.com
Thu Jul 14 14:39:05 CEST 2016
This is a simple R question, but I can't seem to find the answer. I'm
assuming ExperimentHub wants object created by save() and not
In make-data.R, I have a loop where I programmatically make a
GAlignmentPairs object for each of 4 samples. I'm then using assign()
to assign the value to an appropriate name, e.g.
where x is a GAlignmentPairs object I've made.
I'm having trouble though saving this to a file. My first try was:
But this gives:
Error in save(sample.name[i], file = ...
object 'sample.name[i]' not found
I also tried get(), but it's also giving the "not found" error.
On Thu, Jun 30, 2016 at 6:41 PM, Obenchain, Valerie
<Valerie.Obenchain at roswellpark.org> wrote:
> Hi Mike,
> Yes, let's go the ExperimentHub route. The focus is on detailed
> documentation / real use cases so the vignette you describe sounds like
> a good fit.
> Essentially you'll put a package together that is very similar to an
> experimental data package with a few extra files described in the
> ExperimentHubData vignette:
> Let me know when you've got the data objects ready and I'll put them in
> S3. Once that's done we'll test the package functions and put the
> package through a review on the new tracker.
> On 06/30/2016 09:27 AM, Michael Love wrote:
> > I want to generate an experimental data package with a small subset of
> > alignments. The end goal is a software vignette, where the user would
> > specify BAM files. I'd like to try out the ExperimentHub submission
> > process, which is for R data objects. Does it sound reasonable if I
> > were to have an initial code chunk that loads GAlignments and writes
> > out BAM files using rtracklayer::export to then show the use of
> > software with BAM files? There would be so few alignments that it
> > wouldn't be a large computational or storage expense. Or should I
> > submit a standard Bioc experimental data package with files in
> > inst/extdata?
> > _______________________________________________
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