[BioC] known gene => gene symbol for UCSC

[Ido Tamir]

Hi,
how is one supposed to go from ucsc known gene id to gene symbols.

> cols(TxDb.Mmusculus.UCSC.mm9.knownGene)
 [1] "CDSID"      "CDSNAME"    "CDSCHROM"   "CDSSTRAND"  "CDSSTART"
 [6] "CDSEND"     "EXONID"     "EXONNAME"   "EXONCHROM"  "EXONSTRAND"
[11] "EXONSTART"  "EXONEND"    "GENEID"     "TXID"       "EXONRANK"
[16] "TXNAME"     "TXCHROM"    "TXSTRAND"   "TXSTART"    "TXEND"

I don't see anything that would me allow to link this with e.g. Mus.musculus

> select(txdb, keys=c(100009600), cols=cols(txdb) ,keytype="GENEID")
     GENEID  CDSID CDSNAME CDSCHROM CDSSTRAND CDSSTART   CDSEND EXONID EXONNAME
1 100009600 112799    <NA>     chr9         - 20871384 20871523 129355     <NA>
2 100009600 112798    <NA>     chr9         - 20870468 20870821 129354     <NA>
3 100009600 112797    <NA>     chr9         - 20867758 20867840 129353     <NA>
4 100009600 112796    <NA>     chr9         - 20867338 20867431 129352     <NA>
5 100009600 112795    <NA>     chr9         - 20867032 20867161 129351     <NA>
  EXONCHROM EXONSTRAND EXONSTART  EXONEND  TXID EXONRANK     TXNAME TXCHROM
1      chr9          -  20871384 20872369 28943        1 uc009veu.1    chr9
2      chr9          -  20870468 20870821 28943        2 uc009veu.1    chr9
3      chr9          -  20867758 20867840 28943        3 uc009veu.1    chr9
4      chr9          -  20867338 20867431 28943        4 uc009veu.1    chr9
5      chr9          -  20866837 20867161 28943        5 uc009veu.1    chr9
  TXSTRAND  TXSTART    TXEND
1        - 20866837 20872369
2        - 20866837 20872369
3        - 20866837 20872369
4        - 20866837 20872369
5        - 20866837 20872369

> cols(Mus.musculus)
 [1] "GOID"         "TERM"         "ONTOLOGY"     "DEFINITION"   "ENTREZID"
 [6] "PFAM"         "IPI"          "PROSITE"      "ACCNUM"       "ALIAS"
[11] "CHR"          "CHRLOC"       "CHRLOCEND"    "ENZYME"       "PATH"
[16] "PMID"         "REFSEQ"       "SYMBOL"       "UNIGENE"      "ENSEMBL"
[21] "ENSEMBLPROT"  "ENSEMBLTRANS" "GENENAME"     "UNIPROT"      "GO"
[26] "EVIDENCE"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL"  "MGI"
[31] "CDSID"        "CDSNAME"      "CDSCHROM"     "CDSSTRAND"    "CDSSTART"
[36] "CDSEND"       "EXONID"       "EXONNAME"     "EXONCHROM"    "EXONSTRAND"
[41] "EXONSTART"    "EXONEND"      "GENEID"       "TXID"         "EXONRANK"
[46] "TXNAME"       "TXCHROM"      "TXSTRAND"     "TXSTART"      "TXEND"


> select(Mus.musculus,keys="uc009veu.1", cols=c("SYMBOL"), keytype="TXNAME")
Error in .testIfKeysAreOfProposedKeytype(x, keys, keytype) :
  None of the keys entered are valid keys for the keytype specified.

thank you very much,
ido