[Bioc-devel] Experimental data package or ExperimentHub

Michael Love michaelisaiahlove at gmail.com
Thu Jul 14 14:39:05 CEST 2016

dear Valerie,

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.

assign(sample.name[i], x)

where x is a GAlignmentPairs object I've made.

I'm having trouble though saving this to a file. My first try was:

save(sample.name[i], file=paste0(sample.name[i],".rda"))

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.

save(get(sample.name[i]), file=paste0(sample.name[i],".rda"))


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:
> http://www.bioconductor.org/packages/3.4/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHubData.html
> 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.
> Val
> 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?
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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