[Bioc-devel] Experimental data package or ExperimentHub
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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