Great, thanks for this valuable contribution. I made some comments on the commits. The biggest issue is that I think there is a lot of code duplication between the EnsDb and TxDb methods. We should try hard to reduce this.
Michael On Tue, Dec 15, 2015 at 1:37 AM, Rainer Johannes <johannes.rai...@eurac.edu> wrote: > OK, the modifications are in the repositories: > https://github.com/jotsetung/biovizBase > https://github.com/jotsetung/ggbio > > let me know if I can be of any help. > > cheers, jo > > > > On 14 Dec 2015, at 16:00, Rainer Johannes <johannes.rai...@eurac.edu> wrote: > > I’ll do, thanks for all comments! > > > On 14 Dec 2015, at 15:55, Jim Hester <james.f.hes...@gmail.com> wrote: > > Rainer, > > Pull requests to the git mirrors will be closed automatically because they > are read only mirrors. However you can still fork the mirror yourself and > commit your changes to your fork to make them easy for Michael and Tengfei > to review. > > Jim > > On Mon, Dec 14, 2015 at 9:03 AM, Rainer Johannes <johannes.rai...@eurac.edu> > wrote: >> >> dear Micheal, >> >> github pull requests would also be my favorite way to contribute, but >> unfortunately the Bioconductor-mirror github repos are read-only (thus, as >> far as I got it, no pull requests are possible), and I didn’t find other >> repos in github. >> >> Regarding the filtering, you mean implementing subset() and sort() in >> ensembldb? >> My only concern with the approach you describe below is that it rather >> looks like "fetch from db and then filter”, which might be quite slow. I >> implemented the filters such that they are considered at query execution >> time (in fact, they are used to build the SQL query). >> That way also plotting of gene models in ggbio using EnsDbs is really fast >> (since only that small portion that will be plotted is really fetched from >> the db). >> >> thanks, jo >> >> > On 14 Dec 2015, at 14:46, Michael Lawrence <lawrence.mich...@gene.com> >> > wrote: >> > >> > Sounds very useful. Perhaps you could make a github pull request on >> > the Bioconductor mirrors of those packages. Then Tengfei or I could >> > look it over. >> > >> > Btw, I like the filtering functionality in ensemldb. Would be nice to >> > have something as rich for TxDb. Would be great if there were >> > convenience wrappers like subset() and sort(). Like >> > transcripts(sort(subset(db, seqname == "chr1"), by = geneSymbol)). >> > >> > Thanks, >> > Michael >> > >> > On Mon, Dec 14, 2015 at 4:12 AM, Rainer Johannes >> > <johannes.rai...@eurac.edu> wrote: >> >> Dear all, >> >> >> >> I’ve modified the biovizBase and ggbio packages so that they do >> >> directly support EnsDb annotations (just like annotations provided by TxDb >> >> objects/packages). >> >> Is there a way I could provide these changes? I’ve directly contacted >> >> Tengfei last week, but did not get any reply yet… >> >> >> >> cheers, jo >> >> _______________________________________________ >> >> Bioc-devel@r-project.org mailing list >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel