[BioC] rs ids Retrieval using biomaRt

[Ovokeraye Achinike-Oduaran]

Hi all,

I've been trying to retrieve SNP rsids using biomaRt for a number of
SNPs where I have their positions. My input file looks like this:

1 888899000 888899000

where,
1 = chromosome number and the second and third numbers are the
position of the SNP.

My code looks like this:

library(biomaRt)
mart2 = useMart(biomart="snp", dataset="hsapiens_snp")
AFRASN=read.delim("AFR_ASN_neg8P_no_rsids.txt", header = TRUE)
results = getBM(attributes = c("refsnp_id", "allele","chr_name",
	"chrom_strand","consequence_type_tv"),
	filters = "chromosomal_region", values = AFRASN$CHR, mart = mart2)

I must be doing something wrong because it's not working for me. Any
suggestions will be greatly appreciated.

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_.1252  LC_CTYPE=English_.1252
[3] LC_MONETARY=English_.1252 LC_NUMERIC=C
[5] LC_TIME=English_.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.12.0

loaded via a namespace (and not attached):
[1] RCurl_1.91-1.1 XML_3.9-4.1
>

Regards,

Avoks