[R] RSNPper SNPinfo and making it handle a vector

[David Duffy]

"Farrel Buchinsky" <fjbuch at gmail.com> wrote:

> I tried biomaRt
> 
> library(biomaRt)
> ensnp = useMart("snp", dataset = "hsapiens_snp")
> snp = getSNP(chromosome = 17, start = 73649033, end = 73679033, mart = 
> ensnp)
> show(snp)
> 
> Gave me a nice table but it did not seem to permit starting from the point 
> of knowing the SNP and entering a list of rs######. I guess I could always 
> fudge around. But it does not provide the one-stop I was looking for.

Try, for example,

getBM(attributes=c("refsnp_id","chr_name","chrom_start",
                    "ensembl_external_gene_id","allele",
                    "validated"),
       filter="refsnp",
       values=(refsnp=c("rs17166282","rs3897937")), mart=ensnp)


-- 
| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v