I've also found https://github.com/dpryan79/ChromosomeMappings useful
On Thu, Dec 17, 2015 at 6:40 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Michael, > > On 12/17/2015 02:45 PM, Michael Lawrence wrote: >> >> Seems like seqlevelsStyle<- between e.g. UCSC and NCBI does not work >> outside of the "standard" chromosomes. Since GRCh38 (NCBI) and hg38 >> (UCSC) are the same assembly, we could probably implement a complete >> mapping, right? > > > Unfortunately, the seqlevelsStyle() getter and setter were designed > from the very beginning to handle only the standard chromosomes. > Changing this is on the TODO list but didn't happen yet because it > requires a complete refactoring. In the mean time, see > ?fetchExtendedChromInfoFromUCSC for how to map GRCh38 seqlevels to > hg38 seqlevels. > > H. > >> >> Michael >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > _______________________________________________ > 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