[BioC] Use of non-exported `clone` function from GenomicRange package

[Steve Lianoglou]

Hi Pete,

On Sun, Mar 23, 2014 at 10:32 PM, Peter Hickey <hickey at wehi.edu.au> wrote:
> Thanks for giving me plenty to think about, Michael. That's very useful. Yes, it does make sense for these constraints to apply to the rowData independent of the CoMeth object. Can you point me in the direction of a class that extends Granges and/or that uses the extraColumnNames generic.

The VRanges classes in the VariantAnnotation package is one such
class. It extends GRanges and adds a few more columns, like 'ref',
'alt' (and more).

I think the method name you want to look for is
"GenomicRanges:::extraColumnSlotNames", although I'm not sure why this
function isn't exported if it's something other packages should be
using / defining methods for.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech