[BioC] rs ids Retrieval using biomaRt

[Ovokeraye Achinike-Oduaran]

Thanks Vincent.

The original code actually was alright. The problem was with my input
file...it had to be colon (:)-separated.

Thanks again.

Regards,

Avoks

On Sat, Nov 3, 2012 at 3:03 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> 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 at 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$CHR gives me an
>> error --"Error in getBM(attributes = c("refsnp_id", "allele",
>> "chr_name", "chrom_strand",  :   If using multiple filters, the
>> 'value' has to be a list...."
>>
>> Thanks again.
>>
>> Regards,
>>
>> Avoks
>> On Sat, Nov 3, 2012 at 1:46 PM, Vincent Carey
>> <stvjc at channing.harvard.edu> wrote:
>> >
>> >
>> > On Sat, Nov 3, 2012 at 6:15 AM, Ovokeraye Achinike-Oduaran
>> > <ovokeraye at gmail.com> wrote:
>> >>
>> >> Hi all,
>> >>
>> >> I've been trying to retrieve SNP rsids using biomaRt for a number of
>> >> SNPs where I have their positions. My input file looks like this:
>> >>
>> >> 1 888899000 888899000
>> >>
>> >> where,
>> >> 1 = chromosome number and the second and third numbers are the
>> >> position of the SNP.
>> >>
>> >> My code looks like this:
>> >>
>> >> library(biomaRt)
>> >> mart2 = useMart(biomart="snp", dataset="hsapiens_snp")
>> >> AFRASN=read.delim("AFR_ASN_neg8P_no_rsids.txt", header = TRUE)
>> >> results = getBM(attributes = c("refsnp_id", "allele","chr_name",
>> >>         "chrom_strand","consequence_type_tv"),
>> >>         filters = "chromosomal_region", values = AFRASN$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
>> >>
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>> >
>> >
>
>