Hi Peter,
Just added support for dbSNP seqlevels style for Human (in
GenomeInfoDb 1.1.9, will become available tomorrow):
library(SNPlocs.Hsapiens.dbSNP.20120608)
myrsids - c(rs2639606, rs75264089, rs73396229, rs55871206,
rs10932221, rs56219727, rs73709730, rs55838886,
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
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
