[Bioc-devel] Candidates for BiocGenerics

Hi Herve,

thanks again for this!

Both affyPLM and oligo have methods for weights().

b

2012/3/7 Herv? Pag?s<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 Herv? Pag?s<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 Herv? Pag?s<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

--
Herv? Pag?s

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

--
Herv? Pag?s

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

--
Herv? Pag?s

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