extending XString to facilitate miRNA editing
1
0
Entering edit mode
@jeremy-leipzig-4924
Last seen 5.4 years ago
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
miRNA miRNA • 700 views
ADD COMMENT
0
Entering edit mode
@michael-lawrence-3846
Last seen 2.3 years ago
United States
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]]
ADD COMMENT

Login before adding your answer.

Traffic: 868 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6