[Bioc-devel] Experimental data package or ExperimentHub

[Kasper Daniel Hansen]

In save() you can use the "list" argument to give object names.  So
  save(list = sample[i], file=paste0(sample.name[i],".rda"))
should work.

Best,
Kasper

On Thu, Jul 14, 2016 at 9:21 AM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Hi,
>
> There may be more elegant ways but here is one solution.
>
> sample.name <- c("ABC_study_provider", "XYZ_study_provider")
> lapply(sample.name,
>     function(xx) {
>         filename <- paste0(xx, ".rda")
>         ## make the GAlignmentPairs
>         ## ...
>         xx <- GAlignmentPairs()
>         save(xx, file=filename)
>     })
>
> Val
>
>
> On 07/14/2016 05:40 AM, Michael Love wrote:
> > 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
> > saveRDS().
> >
> > 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"))
> >
> >
> > thanks
> > Mike
> >
> > 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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