[Bioc-devel] s4 guidance

[Stefano Berri]

Hi.

could somebody give me some guidance and direction?

I started to make a S4 module for bioconductor.
I am stuck to adding values to a slot using a method.

here a proof of concept

The code, class and methods:
############################

setClass (
    Class = 'test',
    representation = representation (
        x = "numeric",
        doubleX = "numeric"
    )   
)

setGeneric(name = "myDouble", function(object){standardGeneric("myDouble")})
setMethod("myDouble", "test", function(object){
        object at doubleX <- 2*object at x
    })

###########################

# then I type

myT <- new(Class = "test", x = c(1,2,3))
# hoping to populate "myDouble" slot
myDouble(myT)
# but if I look into
myT at doubleX
# I get "numeric(0)"


to make it work I have to return the object
{object at doubleX <- 2*object at x; return (object)}
but then it returns the object (with associated "show" method) which I do
not want.


I also struggle to find documentation online on S4. I have "R programming
for bioinformatics" which cover the basics and then a few bits here and
there, but I could not find a nice tutorial and a reference guide...

I have some other questions:
Comparing to other object-oriented programming languages, I expect to find
similar concepts. 
 - Is there a way to hide/encapsulate slots and methods? If I type "myT" and
then press Tab twice it shows all slots that can be read and even written
to! I makes the whole hassle to object oriented programming useless if the
user can overwrite variables, does it not?

Sorry if my questions are naive...

Thanks for your help

Stefano Berri