[BioC] mouse SNPs

Zhu, Julie Julie.Zhu at umassmed.edu
Wed Sep 8 19:18:48 CEST 2010

Hi Galina,

You could use the annotatePeakInBatch function in ChIPpeakAnno package to
annotate the SNP to the nearest gene and whether the SNP is inside the gene
or not.

Best regards,


On 9/8/10 1:04 PM, "Glazko, Galina" <Galina_Glazko at URMC.Rochester.edu>

> 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

More information about the Bioconductor mailing list