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

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Wed Apr 3 15:48:40 CEST 2019

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?


On 4/3/19, 1:19 AM, "Bioc-devel on behalf of Stephen Martin Pederson" <bioc-devel-bounces using r-project.org on behalf of stephen.pederson using adelaide.edu.au> wrote:

    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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