Lots of package do this so probably you're missing a step, e.g., import(Biostrings) or importClassesFrom(Biostrings, DNAStringSet).
What makes you think it's not permissible? Martin On 4/3/19, 1:19 AM, "Bioc-devel on behalf of Stephen Martin Pederson" <[email protected] on behalf of [email protected]> wrote: Hi, I'm really struggling with how to use an S4 class defined in another package, where I would like to define a method for it in my package. By way of simple example, I'd like to use a DNAStringSet to define an expected GC distribution based on a given fragment size. I had defined the method setMethod("getGcDistn", "DNAStringSet", function(myArgs){myBody}) after using setGeneric() to define the generic getGcDistn. When submitting to BioC, I was advised that this is not permissable & I'm trying to figure out what is the best etiquette & best practice. I haven't really turned up much guidance through numerous searches. Do I just write a standard function which checks the class and executes the code as required without using S4 dispatch? (Disclaimer: I'm very easily confused by the simplest things) Thanks in advance, Steve [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
