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Dear all,
I am Vittorio Fortino and I am writing you to kindly ask some information about submitting R packages.
Basically, I would like to publish an R package about a method for operon prediction. It uses some external data in order to carry out a complete working example. The external data are stored in a ".RData" file (it contains dataframes and lists) and the size is about 50Mb.
Should I add it to the fold "data"??
or
Should I define a new "experimental-data" package??
Thanks in advance for your precious help.
Br,
VF
Dear Andrzej,
thank you for quick reply. I have further questions.
My .RData file contains coverage-depth data compiled from RNA-seq data deposited in the GEO database.
"Could I make/publish an experimental-data package containing this coverage-depth data?"
"Where should I insert the geo-reference? "
"Should I submit the two packages separately?"
Thanks in advance for your answer.
VF
Dear Vittorio,
for accessing data from the GEO database you might wish to use the GEOquery Bioconductor package. If you already have prepossessed data files you might want to include a function/script in your experiment data package demonstrating how these objects were obtained. The reference to GEO could be mentioned on the package's man pages and/or the vignette.
Regarding the submission process: you probably need to submit both your packages together, otherwise there might be problems in resolving the dependencies correctly.
Hope this helps.
Best,
Andrzej
Ok, I understand. However, the RNA-seq data available in GEO database were not aligned and I used BOWTIE to make it. Therefore, should I provide the instructions to run BOWTIE ??
The RNAseqData.HNRNPC.bam.chr14 package might provide a good example; check out the manual and scripts/ directories.