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 <hic...@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 > > hic...@wehi.edu.au > http://www.wehi.edu.au > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
