[Bioc-devel] seqlevelsStyle on alternate chromosomes
lawrence.michael at gene.com
Fri Dec 18 13:11:10 CET 2015
Ok. Could it at least issue a warning when some seqlevels are not mappable?
On Thu, Dec 17, 2015 at 3:40 PM, Hervé Pagès <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.
>> Bioc-devel at r-project.org mailing list
> 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: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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