On Wed, Apr 27, 2016 at 10:52 AM, Hervé Pagès wrote:
> On 04/27/2016 04:24 AM, Michael Lawrence wrote:
>>
>> On Tue, Apr 26, 2016 at 11:12 PM, Hervé Pagès
>> wrote:
>>>
>>> Hi,
>>>
>>> I would not discard defining a SummarizedExperiment subclass so quickly.
>>> SummarizedExperiment is very generi
On 04/27/2016 04:24 AM, Michael Lawrence wrote:
On Tue, Apr 26, 2016 at 11:12 PM, 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 SummarizedExperime
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 stor
I agree with Herve that making a subclass (is that the technical term?)
might be a good idea. This is what I would do. And this is what has been
done historically for all the extensions of ExpressionSet and eSet from
Biobase. The issue with a general class like SummarizedExperiment is that
metho
On Tue, Apr 26, 2016 at 11:12 PM, 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 (C
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
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 dev
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 situa
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 s
On 04/26/2016 05:28 PM, Michael Lawrence wrote:
> On Tue, Apr 26, 2016 at 2:16 PM, Martin Morgan
> wrote:
>> >
>> >On 04/26/2016 04:47 PM, Michael Lawrence wrote:
>>> >>
>>> >>On Tue, Apr 26, 2016 at 11:00 AM, Aaron Lun wrote:
...
>>>BiocGenerics. However, if some other hypothetical packa
On Tue, Apr 26, 2016 at 2:16 PM, Martin Morgan
wrote:
>
>
> On 04/26/2016 04:47 PM, Michael Lawrence wrote:
>>
>> On Tue, Apr 26, 2016 at 11:00 AM, Aaron Lun wrote:
>>>
>>> Dear List,
>>>
>>> When a S4 method for the same class is defined in two separate packages
>>> (i.e., under the same generic
On 04/26/2016 04:47 PM, Michael Lawrence wrote:
On Tue, Apr 26, 2016 at 11:00 AM, Aaron Lun wrote:
Dear List,
When a S4 method for the same class is defined in two separate packages
(i.e., under the same generic), and both packages are loaded into a R
session, it seems that the method from t
On Tue, Apr 26, 2016 at 11:00 AM, Aaron Lun wrote:
> Dear List,
>
> When a S4 method for the same class is defined in two separate packages
> (i.e., under the same generic), and both packages are loaded into a R
> session, it seems that the method from the package loaded later clobbers the
> metho
Dear List,
When a S4 method for the same class is defined in two separate packages
(i.e., under the same generic), and both packages are loaded into a R
session, it seems that the method from the package loaded later clobbers
the method from the package loaded first. Is it possible to specific
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