[Bioc-devel] seqlevelsStyle on alternate chromosomes

Hervé Pagès hpages at fredhutch.org
Fri Dec 18 00:40:45 CET 2015

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.


> Michael
> _______________________________________________
> Bioc-devel at 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
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