[Bioc-devel] avoiding clashes of different S4 methods with the same generic
Hervé Pagès
hpages at fredhutch.org
Wed Apr 27 19:14:58 CEST 2016
On 04/27/2016 03:18 AM, Martin Morgan wrote:
>
>
> On 04/27/2016 02:12 AM, Hervé Pagès wrote:
>> Hi,
>>
>> I would not discard defining a SummarizedExperiment subclass so quickly.
>> SummarizedExperiment is very generic and can contain any kind of data.
>> IIUC the csaw package uses SummarizedExperiment to store a particular
>> kind of data (ChIP-seq data) and I believe specialization is a
>> legitimate situation for defining a subclass, even if the subclass is
>> a "straight" subclass i.e. a subclass that doesn't add new slots or
>> doesn't touch the existing slots.
>>
>> OTOH introducing a "straight" subclass only to define one specialized
>> method on it (the "normalize" method in this case) might not be worth
>> it since there is a cost for such class, even if that cost is minimal:
>> a cost for the user (one new container/constructor to deal with) and a
>> cost for the developer (e.g. multiplication of coerce methods).
>>
>> Changing the signature of the normalize() generic in BiocGenerics and
>> introducing dual dispath is of course doable but that means the
>> maintainers of the packages that define methods on this generic are
>> ok with the dual dispatch game and are willing to make the required
>> modifications to their packages. It's an important change and I don't
>> see an easy way to make it happen smoothly (i.e. thru a
>> deprecated/defunct cycle).
>>
>> Here is the list of packages that currently define methods for
>> BiocGenerics::normalize():
>>
>> affyPLM
>> Cardinal
>> codelink
>> CopyNumber450k
>> csaw
>> diffHic
>> EBImage
>> epigenomix
>> MSnbase
>> oligo
>> qpcrNorm
>> scran
>>
>> [Interestingly the scran package defines a default "normalize" method
>> (i.e. a normalize,ANY method)].
>>
>> Whether we make the second argument lightweight or parameterized (which
>> is something that would need to be decided at the level of the generic)
>
> By 'parameterized' I meant that the second argument could have slots or
> not; I'm not sure whether the use was clear. I don't think the generic
> needs to know about parameterization (also, I agree below that there is
> no need for a base class).
The name of the second argument would depend on whether it's lightweight
or parameterized. Could be something like 'with' or 'method' for the
former and 'param' for the latter. Also the man page for the generic
would need to be able to briefly describe that argument and provide some
guidelines to developers. The more consistent the normalize() interface
is across the dozens of methods, the better for the user.
H.
>
>> these packages will break as soon as we change the signature of the
>> generic. So we'll need to wait after the release before this happens.
>>
>> Personally I find the lightweight second argument not particularly
>> intuitive, elegant, or user-friendly. I'd rather type
>> normalizeSwing(se, ...) or normalize(se, SwingParam(...)) than
>> normalize(se, WithSwing(), ...).
>>
>> Last thing: In case of a parameterized second argument, do we really
>> need a virtual normalizeParam class as parent of all the concrete
>> normalizeParam* classes? If so then I guess we would need to have it
>> defined in BiocGenerics but I think we should try hard to not start
>> defining classes in this package (that could take us too far...)
>
> I agree, I don't think a base class or decisions about parameterization
> would be necessary -- create a MerryGoRoundParam() (parameterized with
> horses or not; much safer than swings!) and the
> normalize,SummarizedExperiment,MerryGoRoundParam-method and you're done.
>
> Also wouldn't dispatch with second arg 'missing' or ANY recover current
> behavior? Maybe it would need to be named and at the end to be
> implemented without others buying in.
>
> setGeneric("foo", function(x, y, ...) standardGeneric("foo"))
> ## setGeneric("foo", function(x, ..., y) standardGeneric("foo"))
>
> .A <- setClass("A", representation(x="numeric"))
>
> setMethod("foo", "A", function(x, y, ...) "ImanA")
>
> > foo(.A())
> [1] "ImanA"
>
> For the normalizeSlides etc approach... I agree that it is probably
> easier for users, though maybe many users are following a vignette so
> the benefit is relatively minimal; there is definitely value in using a
> common prefix or suffix (normalize* or *Param()).
>
> Here's what limma does
>
> > normalize<tab>
> normalizeBetweenArrays normalizeQuantiles
> normalizeCyclicLoess normalizeRobustSpline
> normalizeForPrintorder normalizeVSN
> normalizeForPrintorder.rg normalizeVSN.default
> normalizeMedianAbsValues normalizeVSN.EListRaw
> normalizeMedianValues normalizeVSN.RGList
> normalizePath normalizeWithinArrays
>
> and note the complexity in normalizeVSN, where we're back at desiring a
> generic! If one wanted to implement
> normalizeQuantiles,SummarizedExperiment-method then it would be back to
> negotiating with individual package authors to introduce a new
> BiocGenerics.
>
> Martin
>
>>
>> H.
>>
>> On 04/26/2016 03:03 PM, Aaron Lun wrote:
>>> Yes, but "monkeyBars" doesn't have quite the same pithiness for a
>>> package name.
>>>
>>> Anyway, the dual dispatch mechanism sounds most interesting. I assume
>>> that means we'd have to define some sort of base "normalizeParam" class,
>>> and then derive "csawNormParam" and "swingsNormParam" subclasses, so
>>> that specific methods can be defined for each signature.
>>>
>>> - Aaron
>>>
>>> Martin Morgan wrote:
>>>>
>>>> On 04/26/2016 05:28 PM, Michael Lawrence wrote:
>>>>> On Tue, Apr 26, 2016 at 2:16 PM, Martin Morgan
>>>>> <martin.morgan at roswellpark.org> wrote:
>>>>>>>
>>>>>>> On 04/26/2016 04:47 PM, Michael Lawrence wrote:
>>>>>>>>>
>>>>>>>>> On Tue, Apr 26, 2016 at 11:00 AM, Aaron Lun<alun at wehi.edu.au>
>>>> wrote:
>>>> ...
>>>>>>>>>>> BiocGenerics. However, if some other hypothetical package
>>>> (I'll call it
>>>>>>>>>>> "swings", for argument's sake) were to define a normalize()
>>>> method with a
>>>> ...
>>>>>>> I like the dual dispatch method quite a bit (but wonder why we get
>>>> several
>>>>>>> swings but only one csaw? Maybe a csaw implies two participants
>>>>>> [though I
>>>>>>> think I once in a while csaw-ed alone], so a singular csaw and a
>>>>>> pair of
>>>>>>> swings balance out?), partly because it's very easy to extend
>>>>>> (write another
>>>>>>> method) and the second argument can be either lightweight or
>>>>>> parameterized.
>>>>>>>
>>>>> I could go along with the dual dispatch. "Swings" is short for "Set of
>>>>> swings". Usually, there are several swings in a row, but only one
>>>>> see-saw.
>>>>>
>>>>
>>>> Googling for "how many swings per see-saw" took me to
>>>>
>>>> https://www.cpsc.gov//PageFiles/108601/playgrnd.pdf
>>>>
>>>> where it is apparent that swings are much more dangerous than see-saws
>>>> (e.g., 51 matches for "swing" versus 4 for "see-saw"; "Swings ... were
>>>> involved in about 19 ... percent of injuries ... See-saws accounted
>>>> for about three percent"; "Homemade rope, tire, or tree swings were
>>>> also involved in a number of hanging deaths" [no mention of death by
>>>> see-saw]).
>>>>
>>>> I think for the sake of our users, especially our younger users, we do
>>>> not want to consider swings, or even methods on swings, further.
>>>>
>>>> Martin
>>>>
>>>>
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>>>
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>>>
>>
>
>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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