[Bioc-devel] Experimental data package or ExperimentHub

Thu, Jul 14, 2016 6:21 AM

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?

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[Bioc-devel] Experimental data package or ExperimentHub

Thread (3 messages)