[Bioc-devel] Experimental data package or ExperimentHub

[Obenchain, Valerie]

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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