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
>
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