[BioC] extending XString to facilitate miRNA editing

[Jeremy Leipzig]

Hello,
I would like to apply the notion of "edits" on individual reads (as
opposed to pileups or other aggregates) to examine
post-transcriptional miRNA editing.

I was thinking the best way to do this would be to inherit and extend
XString virtual class with named integers.
setClass('XStringWithEdits',
 contains="XString",
 representation(edits="numeric"),
 prototype(edits = NA_integer_)
)

However I would need DNAString, RNAString, (and DNAStringSet and
RNAStringSet) to re-implement this new virtual class. This would allow
me to write methods that alignment-related classes could use to assign
edits to individual reads.

Is there an elegant way of implementing this feature and having those
classes follow a different drummer? Or maybe something like this
already exists?

thx,
jerm

--
Jeremy Leipzig
Bioinformatics Core
The Children's Hospital of Philadelphia
leipzigj at email.chop.edu
(267) 426-1375