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 >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > > >