[BioC] namespace and other developer tools

[Naomi Altman]

Thanks, Jim.  That helps greatly.

--Naomi

At 10:03 AM 12/14/2006, James W. MacDonald wrote:
>Hi Naomi,
>
>Naomi Altman wrote:
>>I have also been foiled by the sophistication of Bioconductor code.
>>Is there a manual that explains namespace and other code-hiding 
>>tools (.e.g generic functions) that would provide some guidance.
>>The beauty of R is that I can hack - when I can find the code.
>
>I don't know of any manual that covers the topic, but there are only 
>a few things you really need to know to find things.
>
>____________________
>NAMESPACE
>____________________
>
>General description:
>http://en.wikipedia.org/wiki/Namespace_%28computer_science%29
>
>R manual info:
>http://cran.r-project.org/doc/manuals/R-exts.html
>See section 1.6
>
>To find/see/use methods in a namespace
>?methods
>?'::'
>
>For example:
>
> > t.test
>function (x, ...)
>UseMethod("t.test")
><environment: namespace:stats>
>
>Not very useful.
>
> > methods("t.test")
>[1] t.test.default* t.test.formula*
>
>    Non-visible functions are asterisked
>
>Getting closer.
>
> > stats:::t.test.default
>
>Will show the function.
>
>____________________
>S4 methods
>____________________
>
>http://www.bioconductor.org/developers/progRef/S4Objects.pdf
>
>Finding things:
>
>?showMethods
>
>In particular the includeDefs argument.
>
>For example:
>
> > library(GOstats)
> > hyperGTest
>standardGeneric for "hyperGTest" defined from package "Category"
>   defined with value class: "HyperGResultBase"
>
>function (p)
>.valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase",
>     "hyperGTest")
><environment: 0x039c1314>
>Methods may be defined for arguments: p
>
>Not very helpful.
>
> > showMethods("hyperGTest", includeDefs=T)
>
>Will show the function(s)
>
>As many BioC packages use both S4 methods and a namespace, you often 
>need to use a combination of the two in order to find things.
>
>Best,
>
>Jim
>
>
>>Thanks,
>>Naomi
>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111