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.obench...@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
