[Bioc-devel] Candidates for BiocGenerics

[Benilton Carvalho]

Hi Herve,

thanks again for this!

Both affyPLM and oligo have methods for weights().

b

2012/3/7 Hervé Pagès <hpages at fhcrc.org>:
> Hi Benilton,
>
>
> On 03/05/2012 08:13 AM, Benilton Carvalho wrote:
>>
>> Thanks, Herve, for everything.. I'll fix oligoClasses so you dont' get
>> the warning on BiocGenerics.
>>
>> Additionally, for a second round of inclusions, could you [please
>> consider adding 'weights' to BiocGenerics as well?
>
>
> Done in BiocGenerics 0.1.13.
>
> Note that there doesn't seem to be any method defined in Bioconductor
> for weights() yet. Please let me know when you add one so I can provide
> a link to it in the man page for the generic. Thanks!
>
> H.
>
>
>>
>> Thank you very much,
>>
>> benilton
>>
>> 2012/3/2 Hervé Pagès<hpages at fhcrc.org>:
>>>
>>> Done in BiocGenerics 0.1.10.
>>>
>>> Summary:
>>>
>>>  - Removed plot and summary generics (already defined in stats4).
>>>
>>>  - Added nrow, ncol, NROW, NCOL, boxplot, image and residuals generics.
>>>
>>>  - Didn't add coef (already defined in stats4).
>>>
>>>  - Didn't add dim either because it's an "internal generic primitive"
>>>    function (like length(), dimnames(), `dim<-`, `dimnames<-`, etc...,
>>>    see ?InternalMethods for the complete list) so it's not needed.
>>>
>>>  - Added a note in ?BiocGenerics about how to request addition of a
>>>    new generic to the package.
>>>
>>> Benilton, 'R CMD check BiocGenerics' will produce a warning because I
>>> put the following invalid link in the man pages for boxplot and image:
>>>
>>>  \link[oligoClasses]{FeatureSet}
>>>
>>> (please do ?BiocGenerics::image so see the context).
>>>
>>> The reason I put this link is that, for every generic, I'm trying to
>>> provide a link to one of the existing methods and also a link to the
>>> class for which this method is defined. In the case of boxplot and
>>> image, the man page points to the method for FeatureSet and this
>>> class is defined in the oligoClasses package, hence the link.
>>> However, for this link to be valid, the FeatureSet alias would need
>>> to be added somewhere in the man pages of the oligoClasses package
>>> (in FeatureSetExtensions-class.Rd it seems).
>>> Can you please take care of this?
>>>
>>> I know I could use something like \link[oligoClasses]{FeatureSet-class}
>>> and that link would be valid but...
>>>
>>> More generally speaking I'd like to encourage developers to make
>>> ?SomeClass work for their class. Many beginners have no idea they need
>>> to do class?SomeClass or ?`SomeClass-class` in order to get to
>>> the man page for a class and ?SomeClass is less typing anyway.
>>> You could argue that class?SomeClass should be for the class and
>>> ?SomeClass for the SomeClass() function but this function, if defined,
>>> should be the constructor for that class and it's probably a good idea
>>> to document it in the same man page as the class. So, to summarize,
>>> putting
>>>
>>> \alias{SomeClass-class}
>>> \alias{SomeClass}
>>>
>>> in the man page for the SomeClass class makes its documentation a little
>>> bit easier to access for a very small extra cost.
>>>
>>> Cheers,
>>> H.
>>>
>>>
>>>
>>> On 03/01/2012 10:24 AM, Benilton Carvalho wrote:
>>>>
>>>>
>>>> Thank you very much Herve! cheers, b
>>>>
>>>> 2012/3/1 Hervé Pagès<hpages at fhcrc.org>:
>>>>>
>>>>>
>>>>> Hi Benilton, Sean,
>>>>>
>>>>>
>>>>> On 03/01/2012 08:18 AM, Sean Davis wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Mar 1, 2012 at 7:57 AM, Benilton Carvalho
>>>>>> <beniltoncarvalho at gmail.com>      wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I'm implementing a few things in oligo and I wonder if it'd make
>>>>>>> sense
>>>>>>> to
>>>>>>> have
>>>>>>>
>>>>>>> boxplot/coef/image/ncol/residuals
>>>>>>>
>>>>>>> defined in BiocGenerics?
>>>>>>>
>>>>>>> If it's only me using them, I'm happy to have everything in oligo.
>>>>>>>
>>>>>>> Thoughts?
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> It seems that if someone is proposing a generic for functionality
>>>>>> already in base R, that generic is by definition a good candidate for
>>>>>> inclusion in BiocGenerics.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I agree.
>>>>>
>>>>>
>>>>>> Are there downsides to having this be a
>>>>>> criterion for inclusion?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Not that I know of.
>>>>>
>>>>> I'll add boxplot, coef, image, ncol and residuals to BiocGenerics
>>>>> today.
>>>>> I'll also add nrow, NROW, NCOL and dim, which are all interconnected
>>>>> with ncol.
>>>>>
>>>>> Cheers,
>>>>> H.
>>>>>
>>>>>
>>>>>>
>>>>>> Sean
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Hervé Pagès
>>>>>
>>>>> Program in Computational Biology
>>>>> Division of Public Health Sciences
>>>>> Fred Hutchinson Cancer Research Center
>>>>> 1100 Fairview Ave. N, M1-B514
>>>>> P.O. Box 19024
>>>>> Seattle, WA 98109-1024
>>>>>
>>>>> E-mail: hpages at fhcrc.org
>>>>> Phone:  (206) 667-5791
>>>>> Fax:    (206) 667-1319
>>>
>>>
>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fhcrc.org
>>> Phone:  (206) 667-5791
>>> Fax:    (206) 667-1319
>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319