I have a list of probesets from the Affymetrix GenomeWideSNP6 chip (e.g. CN_1111671, SNP_A-8305771) and want to annotate them in bioconductor, mainly with genome coordinates. Is there any easy to use annotation package like for the HGU133A chip? I know of NetAFFX, but I would like to circumvent the ex- and import steps. Thanks, Christian

On Mon, Sep 10, 2012 at 7:07 AM, Christian Ruckert <cruckert@uni- muenster.de=""> wrote: > I have a list of probesets from the Affymetrix GenomeWideSNP6 chip (e.g. > CN_1111671, SNP_A-8305771) and want to annotate them in bioconductor, > mainly with genome coordinates. Is there any easy to use annotation package > like for the HGU133A chip? I know of NetAFFX, but I would like to > circumvent the ex- and import steps. > > After installing and attaching pd.genomewidesnp.6 package from metadata branch, you will have access to a SQLite connection > objects(2) [1] "pd.genomewidesnp.6" > getClass(class(pd.genomewidesnp.6)) Class "AffySNPCNVPDInfo" [package "oligoClasses"] Slots: Name: getdb tableInfo geometry manufacturer genomebuild Class: function data.frame integer character character Name: annotation Class: character Extends: Class "AffySNPPDInfo", directly Class "SNPPDInfo", by class "AffySNPPDInfo", distance 2 Class "DBPDInfo", by class "AffySNPPDInfo", distance 3 > con = pd.genomewidesnp.6@getdb() > dbListTables(con) [1] "featureSet" "featureSetCNV" "fragmentLength" [4] "fragmentLengthCNV" "pmfeature" "pmfeatureCNV" [7] "sequence" "sequenceCNV" "sqlite_stat1" [10] "table_info" > dbGetQuery(con, "select * from featureSet limit 3") fsetid man_fsetid affy_snp_id dbsnp_rs_id chrom physical_pos strand 1 1 SNP_A-2131660 NA rs2887286 1 1156131 0 2 2 SNP_A-1967418 NA rs1496555 1 2234251 0 3 3 SNP_A-1969580 NA rs41477744 1 2329564 0 cytoband allele_a allele_b 1 p36.33 C T 2 p36.33 A G 3 p36.32 A G this table has the information you have asked about, and more. you will need to understand the DBI and SQL to emulate, if you wish, the typical annotation resolution facilities. > Thanks, > Christian > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]