[Bioc-devel] RFC: xy2i and i2xy in *cdf packages

Wolfgang Huber <huber at ebi.ac.uk> writes:

Hi,

Rather than make up these new dimension objects in the CDF package,
why not teach the affy:indices2xy function to reach into the
appropriate CDF package and grab the *unexported*, existing i2xy
function in order to do its thing, and the affy:xy2indices to grab the
*unexported* xy2i function? Seems like the least intrusive way to do
things, and more flexible.

I don't think we should change the visibility of the xy2i functions
without going through the deprecation cycle.

But in general, I like your suggestion.  Teaching affy to grab the
appropriate function seems sensible.  Personally, I think it is fine
to have these functions exported.  You can still get the right one
when using affy::xy2indices.  Symbol masking is a fact of R.

But having the dimensions accessible in the CDF package also makes
sense to me and is easy so I'm still in favor of adding hgu95av2dim.
And the xy2i and i2xy functions should use it...

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org