[Bioc-devel] seqlevelsStyle on alternate chromosomes
I've also found https://github.com/dpryan79/ChromosomeMappings useful
On Thu, Dec 17, 2015 at 6:40 PM, Herv? Pag?s <hpages at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel