On 03/11/2021 2:54 p.m., Andrew Simmons wrote:
First, your signature for names.pm is wrong. It should look something more
like:


names.pm <- function (x)
{
}


As for the body of the function, you might do something like:


names.pm <- function (x)
{
     NextMethod()
}


but you don't need to define a names method if you're just going to call
the next method. I would suggest not defining a names method at all.


As a side note, I would suggest making your class through the methods
package, with methods::setClass("pm", ...)
See the documentation for setClass for more details, it's the recommended
way to define classes in R.

That's incorrect. It is *a* recommended way to define classes in R, but there are other recommended ways as well, for doing other kinds of things, and many people stick with the S3 system without formal classes at all.

If you're writing a Bioconductor package you should probably use the formal methods. If you're writing code for other purposes, you should think about whether you need formal classes at all, and if so, whether the methods package formalism is a match for what you're doing.

Duncan Murdoch

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