Thanks for the explanation, Vincent. GenomeInfoDb has NCBI and UCSC support, but doesn't seem to support the dbSNP format. Perhaps this should be added?
> seqlevelsStyle(seqnames(SNPlocs.Hsapiens.dbSNP.20120608)) Error in .guessSpeciesStyle(seqnames) : The style does not have a compatible entry for the species supported by Seqname. Please see genomeStyles() for supported species/style On 18/06/2014, at 12:40 PM, Vincent Carey <[email protected]> wrote: > 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 <[email protected]> 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 > > [email protected] > http://www.wehi.edu.au > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:28}} _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
