it is the convention used in dbSNP, just propagated directly.  indeed one
typically has to relabel, but there
is seqnamesStyle infrastructure in GenomeInfoDb that may help.


On Tue, Jun 17, 2014 at 8:17 PM, Peter Hickey <hickey@wehi.edu.au> wrote:

> Is there a reason why the seqnames of SNPlocs.Hsapiens.dbSNP.20120608 (and
> possibly the other SNPlocs.*) use the prefix "ch" instead of "chr"? E.g.
> "ch1" instead of "chr1". It doesn't seem to fit with any standard way of
> naming chromosomes and means that these need to be renamed to use with most
> other Bioconductor data sources.
> Thanks,
> Pete
> --------------------------------
> Peter Hickey,
> PhD Student/Research Assistant,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> Ph: +613 9345 2324
>
> hickey@wehi.edu.au
> http://www.wehi.edu.au
>
>
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