[Bioc-devel] Delayed Assignment to S4 Slots

[Hervé Pagès]

The constructor should probably be doing something like this but you get 
the idea:

   ResubstituteParams <- function(nFeatures_call)
   {
     if (missing(nFeatures_call))
         new("ResubstituteParams", nFeatures=seq(10, 100, 10))
     else
         new("ResubstituteParams", 
nFeatures_call=substitute(nFeatures_call))
   }


H.

On 15/10/2021 14:41, Hervé Pagès wrote:
> Hi Dario,
> 
> It would be good if you could provide a little bit more context about 
> ResubstituteParams objects and how they are typically used in practice.
> 
> As you found out, delayedAssign() won't work. How about trying something 
> like this?
> 
>    setClassUnion("numeric_OR_NULL", c("numeric", "NULL"))
> 
> 
> 
>    setClass("ResubstituteParams",
> 
>      slots=c(
> 
>          nFeatures_call="call",
> 
>          nFeatures="numeric_OR_NULL"
> 
>      )
> 
>    )
> 
> 
> 
>    ResubstituteParams <- function(nFeatures_call)
> 
>    {
> 
>      new("ResubstituteParams", nFeatures_call=substitute(nFeatures_call))
> 
>    }
> 
> 
> 
>    ## Should preferrably be an S4 generic with a method for
>    ## ResubstituteParams
>   objects.
> 
>    nFeatures <- function(x)
> 
>    {
> 
>      if (!is.null(x using nFeatures))
> 
>          return(x using nFeatures)
> 
>      eval(x using nFeatures_call)
> 
>    }
> 
> 
> 
>    r <- ResubstituteParams(nrow(measurements))
> 
>    measurements <- matrix(1:100, ncol=10)
> 
>    nFeatures(r)
> 
>    # [1] 10
> 
> Accessor functions are not just a nice way to hide the internals of your 
> object but they are also a powerful way to take full control of what 
> needs to happen exactly when a user tries to access a particular part of 
> your object, whether that part lives in a slot, a combination of slots, 
> or in no slot at all.
> 
> 
> Cheers,
> H.
> 
> 
> On 13/10/2021 21:00, Dario Strbenac via Bioc-devel wrote:
>> Good day,
>>
>> I have an S4 class with some slots in my Bioconductor package. One of 
>> the slots stores the range of top variables to try during feature 
>> selection (the variables might be ranked by some score, like a 
>> t-test). The empty constructor looks like
>>
>> setMethod("ResubstituteParams", "missing", function()
>> {
>>    new("ResubstituteParams", nFeatures = seq(10, 100, 10), 
>> performanceType = "balanced error")
>> })
>>
>> But, someone might have a small omics data set with only 40 features 
>> (e.g. CyTOF). Therefore, trying the top 10, 20, ..., 100 is not a good 
>> default. A good default would wait until the S4 class is accessed 
>> within cross-validation and then, based on the dimensions of the 
>> matrix or DataFrame, pick a suitable range. I looked at delayedAssign, 
>> but x is described as "a variable name (given as a quoted string in 
>> the function call)". It doesn't seem to apply to S4 slots based on my 
>> understanding of it.
>>
>>> r <- ResubstituteParams()
>>> delayedAssign("r using nFeatures", nrow(measurements))
>>> measurements <- matrix(1:100, ncol = 10)
>>> r using nFeatures # Still the value from empty constructor.
>>   [1]  10  20  30  40  50  60  70  80  90 100
>>
>> --------------------------------------
>> Dario Strbenac
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com