just a little bit more followup > library(SNPlocs.Hsapiens.dbSNP.20100427) > c21 = getSNPlocs("ch21") > names(c21) [1] "RefSNP_id" "alleles_as_ambig" "loc" > c21[ c21$RefSNP_id == 4591, ] RefSNP_id alleles_as_ambig loc 164200 4591 R 35281393 > sessionInfo() R version 2.12.0 Under development (unstable) (2010-05-03 r51901) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] SNPlocs.Hsapiens.dbSNP.20100427_0.99.2 [2] GenomicRanges_1.1.7 [3] IRanges_1.7.0 [4] pd.genomewidesnp.6_1.0.0 [5] oligoClasses_1.11.0 [6] Biobase_2.9.0 [7] RSQLite_0.8-4 [8] DBI_0.2-5 loaded via a namespace (and not attached): [1] Biostrings_2.17.0 affyio_1.17.0 tools_2.12.0 On Thu, May 6, 2010 at 10:17 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > This is a complex question and there are perhaps no fully satisfying > approaches. Note that the task of reannotating the affy chip is not a > concern of any Bioconductor software. But there are resources that may > help. Making an immense query to Biomart seems unwise but others may have > other views. > > You may wish to take note of the package > > SNPlocs.Hsapiens.dbSNP.20100427 > > available from Bioconductor. It includes SNP metadata with provenance > > "The source data files used for this package were created by NCBI on 24-26 > March 2010. > > WARNING: The SNPs in this package are based on the GRCh37 genome. Note that > the GRCh37 > genome is the same as the hg19 genome from UCSC except for the > mitochondrion chromosome. > > Therefore, the SNPs in this package can be "injected" in > BSgenome.Hsapiens.UCSC.hg19 but this > injection will exclude chrM (i.e. nothing will be injected in that > sequence). > > See http://www.ncbi.nlm.nih.gov/snp, the SNP Home at NCBI, for more > information > about dbSNP. > > See ?injectSNPs in the BSgenome software package for more information about > the SNP injection > mechanism. > See http://genome.ucsc.edu/cgi- bin/hgGateway?clade=mammal&org=Human&db= > hg19 for more information about the Human Feb. 2009 (GRCh37/hg19) assembly > used by the > UCSC Genome Browser." > > clearly noted in the Reference manual pages for the package, accessible at > > > http://www.bioconductor.org/packages/release/data/annotation/html/SN Plocs.Hsapiens.dbSNP.20100427.html > > if you take the time to learn how to work with the SNPlocs package, you > will be able to get more current location data in various formats. A > discussion of how to bring that information in the context of reannotating > the 6.0 chip requires much more information regarding objectives. > > On Thu, May 6, 2010 at 9:51 AM, Kay Jaja <kjaja27@yahoo.com> wrote: > >> Hi , >> >> I have downloaded the Affy6.0 snp annotation file from Affy website but >> the snps are maped to an old build. for example, rs2834296 is mapped to chr >> 21 and base pair position 34203263, but if you go to Ensembl you will find >> this snp has a different name rs4591 and the base pair is 35281393. >> I needed to remap all the snps to the current build so I tried biomart >> package using R using the scrip below >> >> mart <- useMart("snp") >> mart<-useDataset("hsapiens_snp",mart) >> out=getBM(attributes=c("refsnp_id","chr_name","chrom_start"), >> filters=c("refsnp"), values=snps, mart=mart) >> >> >> here is the problem >> >> snps is a vector of rs# from the Affy 6.0 ( there are about 900,000) snps >> but the script took forever was never finished. >> I tried to have the vector snps to be the only the rs# from chr 21, but >> not all the snps get mapped for example the above snps that i mentioned >> before rs2834296 will be dropped. >> >> >> any ideas on how to map the snps in the affy 6.0 to the current build >> >> thanks and appreciate your help >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]