[Bioc-devel] How to define S4 method for class from another package

Stephen Martin Pederson @tephen@peder@on @end|ng |rom @de|@|de@edu@@u
Wed Apr 3 07:19:07 CEST 2019


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,


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