It's a little hard to follow the details of the conversation on your
submission, but maybe I find myself disagreeing with the reviewer __
In some ways one would like to think 'I can find out everything I need to know
about DNAStringSet by looking in Biostrings', but as your use case illustrates
there are things that people want to do that are not defined in Biostrings. It
would be wrong to create a new class MyDNAStringSet that has no new data
representation just new methods, and it would be wrong to create an entirely
new class with just your methods, and it would be wrong to say 'well, if you
want to calculate the GC distribution of a DNAStringSet, just copy and paste
these lines of code...', and it would be wrong (at least in general) to add all
kinds of idiosyncratic code to Biostrings 'on request' of other package
authors. So the only thing left is to write new methods in your package that
use data structures from other packages.
On the technical side of things, if the existing class and methods are as
strongly S4 based as DNAStringSet, I would not implement S3 methods. So
setGeneric("getGcDistn", function(x) standardGeneric("getGcDistn"))
setMethod("getGcDistn", "ANY", function(x) { ... })
setMethod("getGcDistn", "character", function(x) { ... })
setMethod("getGcDistn", "DNAStringSet", function(x) { ... })
S3 methods are relevant when there are S3 generics or S3 classes ('character'
is a base type) that one wants to handle, so not relevant in the current
circumstance; `sort()` and the GenomicRanges package would be an example of
this. `sort()` is an S3 generic in base R, but is also an S4 generic in
BiocGenerics. So we have
> library(GenomicRanges)
> methods(sort)
[1] sort,ANY-method sort,DataTable-method
[3] sort,GenomicRanges-method sort,GRangesList-method
[5] sort,List-method sort,Rle-method
[7] sort,SortedByQueryHits-method sort,Vector-method
[9] sort.bibentry* sort.default
[11] sort.GenomicRanges sort.GRangesList
[13] sort.POSIXlt sort.Vector
see '?methods' for accessing help and source code
with both S3 and S4 methods for, e.g., GenomicRanges and GRangesList.
Martin
On 4/3/19, 10:17 AM, "Stephen Martin Pederson"
<[email protected]> wrote:
Hi Martin,
Thanks for the help. Everything was working, despite missing methods for
signature = "ANY" (which is now fixed).
It was just the
feedback given when submitting & when I sought clarification to ease my
confusion, that was confirmed as the interpretation. I've just re-implemented
that particular one using S3 dispatch using the functions getGcDistn.default,
getGcDistn.character, getGcDistn.DNAStringSet,
based on a modification of your reply here:
https://stackoverflow.com/questions/12100856/combining-s4-and-s3-methods-in-a-single-function.
The original discussion which made me think it's not permissable is here:
https://github.com/Bioconductor/Contributions/issues/985#issuecomment-468003572
Thanks again,
Steve
________________________________________
From: Martin Morgan <[email protected]>
Sent: Thursday, 4 April 2019 12:18 AM
To: Stephen Martin Pederson; [email protected]
Subject: Re: [Bioc-devel] How to define S4 method for class from another
package
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
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