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

I guess I'm wondering if you really need the edits tied to the sequence data or if positional information in an interval data structure (like GRanges) is sufficient. One way one could overlay "marks" like this on an XString is to use the mask feature. Not sure if that would work for you, but it might be expedient. It would also integrate with the ranges infrastructure. Michael On Fri, Oct 21, 2011 at 1:02 PM, Jeremy Leipzig <leipzig@gmail.com> wrote: > 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@email.chop.edu > (267) 426-1375 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]