R provides a syntax for manipulating data. That syntax can be readily mapped to other languages. Once an idea has been vetted and tested, developers can resort to implementation of critical code sections in other languages, such as C, to improve performance. For instance, the Ranges infrastructure has gone through many iterations of this process. Alternatively, as we have done with the Rsamtools package, R's foreign language interfaces can be exploited to access an established software library from within R. This has allowed high-level code written in R to seamlessly use the functionality of the SAMtools software [19].
