[BioC] known gene => gene symbol for UCSC
James W. MacDonald
jmacdon at uw.edu
Tue Apr 2 15:49:29 CEST 2013
Hi Ido,
You don't give sessionInfo() results, but this works for me
> select(Mus.musculus, "uc009veu.1", "SYMBOL","TXNAME")
TXNAME SYMBOL
1 uc009veu.1 Zglp1
> sessionInfo()
R Under development (unstable) (2013-01-22 r61734)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Mus.musculus_1.1.0
[2] TxDb.Mmusculus.UCSC.mm10.knownGene_2.9.0
[3] org.Mm.eg.db_2.9.0
[4] GO.db_2.9.0
[5] RSQLite_0.11.2
[6] DBI_0.2-5
[7] OrganismDbi_1.1.14
[8] GenomicFeatures_1.11.16
[9] GenomicRanges_1.11.44
[10] IRanges_1.17.42
[11] AnnotationDbi_1.21.16
[12] Biobase_2.19.3
[13] BiocGenerics_0.5.6
loaded via a namespace (and not attached):
[1] biomaRt_2.15.1 Biostrings_2.27.14 bitops_1.0-5
[4] BSgenome_1.27.1 graph_1.37.7 RBGL_1.35.0
[7] RCurl_1.95-4.1 Rsamtools_1.11.27 rtracklayer_1.19.11
[10] stats4_3.0.0 tools_3.0.0 XML_3.96-1.1
[13] zlibbioc_1.5.0
On 4/2/2013 9:43 AM, Ido Tamir wrote:
> 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
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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