[BioC] formal methods and classes and capitalization conventions

[Gordon Smyth]

I'd like to raise the issue of a capitalization convention for naming 
objects in R. Almost everything in R used to be lowercase but recently 
there is increasing use of mixed upper/lower case to define names. There is 
potential for using the capitalizations to make code more self explanatory, 
but only if a consistent system is used.

In Java, capitalization is used to indicate the type of object. Names of 
methods are capitalized except for the first word (e.g., geneNames), names 
of classes are fully capitalized (e.g., ExprSet), names of data objects are 
all lowercase, and names of libraries have their own conventions but 
normally with lowercase letters. A programmer can recognize the type of 
object in many cases simply from the name.

In R, Java capitalization has started to be used for formal generic 
functions, but the point of the convention is being lost because the same 
capitalization is being used for classes, non-generic functions, package 
names and even function arguments. Naming is not always done consistently 
and different conventions seem to be used by different people, so within 
Bioconductor we have classes, functions, arguments, and packages with lots 
of different capitalization styles. One cannot predict what capitalization 
style will be used for a given object, so capitalization is on the way to 
being a complication rather than a clarification.

Here is a suggestion for a convention, which people can shoot down if they 
like:

Classes: full capitalization, e.g., ExprSet, AffyBatch, MarrayNorm
Generic functions: lower case first word, e.g., maNorm, normalize, rma, 
geneNames
Non-generic functions: lowercase, possibly with dot separaters
Members of data classes: lowercase, possibly with dot separaters
Function arguments: lowercase, possibly with dot separaters
Packages: lowercase, e.g., affy, marraynorm

Cheers
Gordon