[Bioc-devel] Creating Biostrings DNAStringSet from Rcpp/C++

Michael Lawrence lawrence.michael at gene.com
Tue Jan 5 14:31:03 CET 2016

You're going to want to use the Biostrings C API. You can see
TwoBitFile_read() in src/twoBit.c in rtracklayer for an example. It's
not trivial.


On Tue, Jan 5, 2016 at 5:21 AM, Sean Davis <seandavi at gmail.com> wrote:
> Forgive the really naive questions, but my C/C++ and Biostrings skills are
> pretty rough.  I have been playing with Rcpp to interface to an external
> library for reading sequence formats.  I am reading DNA sequences
> one-at-a-time and would like to package a set of those up as a DNAStringSet.
> I have at least two options:
> 1) Return a character vector back to R and then create a DNAStringSet in R.
> This works now and works fine.
> 2) Create the DNAStringSet in the cpp code.
> Are there advantages to using choice #2?  If so, where would I start to get
> the necessary Rcpp/Biostrings glue in place? I know how to make new S4
> objects in Rcpp, so it is really a question of knowing what class hierarchy
> I need to instantiate and, roughly, how.  Any pointers or code examples?
> Thanks,
> Sean
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