My pleasure, Tim  :) And thank you, Vince, for the very useful information. K --- On Mon, 8/15/11, Tim Triche, Jr. <tim.triche@gmail.com> wrote: From: Tim Triche, Jr. <tim.triche@gmail.com> Subject: Re: [BioC] To find rsIDs To: "Vincent Carey" <stvjc@channing.harvard.edu> Cc: "khadeeja ismail" <hajjja@yahoo.com>, bioconductor@r-project.org Date: Monday, August 15, 2011, 8:52 AM woohoo, a twofer!  I can finish modernizing 450k.db and do something I told Vince I'd take a whack at long before I learned how to properly use Biostrings, GenomicRanges, and the BSgenome packages. This type of request ought to be made into a vignette, so it will be. Thanks for the suggestion Khadeeja. On Sun, Aug 14, 2011 at 12:06 PM, Vincent Carey <stvjc@channing.harvard.edu> wrote: I don't find this question particularly clear.  I believe the key resources will be the IlluminaHumanMethylation450k.db packages and the appropriate SNPlocs.Hsapiens.dbSNP.* SNP location package. Once you have installed IlluminaHumanMethylation450k.db, you can use SQL queries to obtain information about the probes or associated islands. The vignette of the package is also relevant.  Coordinates are given for probes, against two genome builds.  Some information relevant to your concern may be in the "snp" and "snp10" columns but I do not know where these are documented. After installing and attaching IlluminaHumanMethylation450k.db, one way to proceed is > con = IlluminaHumanMethylation450k_dbconn() > dbListTables(con)  [1] "accessions"     "controlprobes"  "cpgi"           "cpgilocation"  [5] "cpgirelations"  "cpgislandnames" "cpgiview"       "dmr"  [9] "fantom"         "featuregroups"  "featurenames"   "map_counts" [13] "map_metadata"   "metadata"       "probedesign"    "probedesign1" [17] "probedesign2"   "probelocation"  "probes"         "probesummary" [21] "reglocation"    "regulatory"     "regview"        "relations" [25] "snps"           "sqlite_stat1" > dbGetQuery(con, "select * from probedesign limit 5")  row_names   Probe_ID Infinium_Design_Type AddressA_ID AddressB_ID 1         1 cg00035864                   II    31729416 2         2 cg00050873                    I    32735311    31717405 3         3 cg00061679                   II    28780415 4         4 cg00063477                   II    16712347 5         5 cg00121626                   II    19779393  Color_Channel Random_Loci Methyl27_Loci Is_HMM_Island NuID CpGs 1          Both           0             0             0 TIRyS37UTIV_D83QPY    2 2           Red           0             0             1 HarUVHUAFFEvub5ddk    4 3          Both           0             0             0 BY6AMCwUDLLg8vfQ7c    1 4          Both           0             0             0 0Y6CT.7AzG9LP_7oIE    3 5          Both           0             0             0 0IcOoun5CUrHuVxB3Y    5  Coordinate_37 Chromosome_37 Coordinate_36 Chromosome_36 Genome_Build enhancer 1       8553009             Y       8613009             Y 37        0 2       9363356             Y       9973356             Y 37        0 3      25314171             Y      23723559             Y 37        0 4      22741795             Y      21151183             Y 37        0 5      21664296             Y      20123684             Y 37        0  dhs snp snp10 strand gene_body 1   0   0     0      F         0 2   0   0     0      R         1 3   0   0     0      R         1 4   0   1     1      F         1 5   0   0     0      R         1 If you are interested in coincidences of SNP with probes or CpG islands, you can use GRanges built from these resources.  Others more directly concerned with these data types can undoubtedly provide more concrete guidance. On Sun, Aug 14, 2011 at 7:39 AM, khadeeja ismail <hajjja@yahoo.com> wrote: > Hi All, > > I have been going through Biostrings, BSgenome.Hsapiens.UCSC.hg19, > GenomicRanges > and SNPlocs.Hsapiens.dbSNP.20101109  to find a way to get the rsIDs of SNPs > on IlluminaHumanMethylation450k data, and so far unsucessful. > > Would be great if anyone could explain how it is done. > > Thanks in advance, > > Khadeeja > >        [[alternative HTML version deleted]] > > > _______________________________________________ > 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 >        [[alternative HTML version deleted]] _______________________________________________ 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 -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann [[alternative HTML version deleted]]