[Bioc-devel] seqlevelsStyle on alternate chromosomes

[Sonali B Arora]

On a slightly similar note,

I also feel that we should have a map available ( possibly in the 
vignette of GenomeInfoDb, under seqlevelsStyle)
something like this 
(http://www.gencodegenes.org/releases/reference_releases.html)
which tells people the corresponding versions between UCSC/NCBI/GENCODE

For Mouse - 
http://www.gencodegenes.org/mouse_releases/reference_releases.html


Thanks and Regards,
Sonali.






On 12/18/2015 4:11 AM, Michael Lawrence wrote:
> Ok. Could it at least issue a warning when some seqlevels are not mappable?
>
> Thanks,
> Michael
>
> 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.
>>
>> H.
>>
>>> 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
>> 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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