arrange for the start and end coordinates to be numerical vectors.  how you
do this in R depends on your file structure and your input call; if
problematic, please query r-help.  once you have acquired the vectors, you
can follow the prescriptions of the man page.  For example

results = getBM(attributes = c("refsnp_id", "allele","chr_name",
        "chrom_strand","consequence_type_tv", "chrom_start"),
        filters = c("chr_name", "chrom_start", "chrom_end"),
values=list("20",
     c(100066, 100134), c(100066, 100134)), mart=mart2)  # replace the two
calls to c() here with
#   your vector(s)

returns two records


On Sat, Nov 3, 2012 at 8:38 AM, Ovokeraye Achinike-Oduaran <
ovokeraye@gmail.com> wrote:

> Thanks Vincent. You are right about the filters. One more thing: how
> would this work with a batch input "values" list i.e reading the
> positions from a file? For example:
>
> CHR
> 1, 11182261, 11182261
> 1, 11264032, 11264032
> 1, 11264036, 11264036
> 1, 11282246, 11282246
> 1, 11292945, 11292945
> 1, 11306660, 11306660
> 1, 11314655, 11314655
>
> Using the same code but specifying values = AFRASN$CHR gives me an
> error --"Error in getBM(attributes = c("refsnp_id", "allele",
> "chr_name", "chrom_strand",  :   If using multiple filters, the
> 'value' has to be a list...."
>
> Thanks again.
>
> Regards,
>
> Avoks
> On Sat, Nov 3, 2012 at 1:46 PM, Vincent Carey
> <stvjc@channing.harvard.edu> wrote:
> >
> >
> > On Sat, Nov 3, 2012 at 6:15 AM, Ovokeraye Achinike-Oduaran
> > <ovokeraye@gmail.com> wrote:
> >>
> >> Hi all,
> >>
> >> I've been trying to retrieve SNP rsids using biomaRt for a number of
> >> SNPs where I have their positions. My input file looks like this:
> >>
> >> 1 888899000 888899000
> >>
> >> where,
> >> 1 = chromosome number and the second and third numbers are the
> >> position of the SNP.
> >>
> >> My code looks like this:
> >>
> >> library(biomaRt)
> >> mart2 = useMart(biomart="snp", dataset="hsapiens_snp")
> >> AFRASN=read.delim("AFR_ASN_neg8P_no_rsids.txt", header = TRUE)
> >> results = getBM(attributes = c("refsnp_id", "allele","chr_name",
> >>         "chrom_strand","consequence_type_tv"),
> >>         filters = "chromosomal_region", values = AFRASN$CHR, mart =
> mart2)
> >>
> >> I must be doing something wrong because it's not working for me. Any
> >> suggestions will be greatly appreciated.
> >>
> >
> > your filter/value spec does not seem valid.  i do not know how to
> determine
> > validity.  but
> > the following yields 23 records
> >
> > results = getBM(attributes = c("refsnp_id", "allele","chr_name",
> >         "chrom_strand","consequence_type_tv"),
> >         filters = c("chr_name", "chrom_start", "chrom_end"),
> > values=list("20",
> >      100000, 101000), mart=mart2)
> >
> >
> >>
> >> > 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
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
>

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