[BioC] mouse SNPs

[Vincent Carey]

What do you mean by "annotate"?  Your best bet for a programmatic
attack is probably biomaRt

library(biomaRt)
listMarts()
mm = useMart("snp")
listDatasets(mm)
ds = useDataset("mmusculus_snp", mart=mm)
listAttributes(ds)

then the fun begins with getBM...


On Wed, Sep 8, 2010 at 1:04 PM, Glazko, Galina
<Galina_Glazko at urmc.rochester.edu> wrote:
> Dear list,
>
> I have annotation question and just hope that someone had already similar problem and
> would be willing to share the experience.
>
> I have about 100 mouse SNPs in the format:
>
> Chromosome number     SNP coordinate
> (for example:)
> 16                                 69067865
>
> I need to annotate them, in order to understand whether they are functional or not.
> I can go one-by-one through UCSC (http://www.genome.ucsc.edu/)
> and annotate them, but I hope that may be someone already did something similar
> and has better ideas about how to do it faster, probably using Bioconductor?
> And also, may be there are specific resources available for mouse SNPs annotation?
> There is mouse HapMap, but it is just a collection of SNPs in different strains and nothing else.
>
> I would really appreciate your suggestions!
> best regards
> Galina
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>