[BioC] known gene => gene symbol for UCSC

Ido Tamir tamir at imp.ac.at
Tue Apr 2 16:20:55 CEST 2013


Dear James,

thank you very much. It did not work with:
a fresh session (a) and an old session (b)

Your packages seem newer, but my ids are from the old package, so they
should be consistent.
I just installed the bioconductor packages Mus.musculus and  TxDb.Mmusculus.UCSC.mm10.ensGene today.

best,
ido

a) fresh session
> sessionInfo()
R version 2.15.1 (2012-06-22)
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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Mus.musculus_1.0.0
[2] TxDb.Mmusculus.UCSC.mm10.ensGene_2.8.0
[3] org.Mm.eg.db_2.8.0
[4] GO.db_2.8.0
[5] RSQLite_0.11.2
[6] DBI_0.2-5
[7] OrganismDbi_1.0.3
[8] GenomicFeatures_1.10.2
[9] GenomicRanges_1.10.7
[10] IRanges_1.16.6
[11] AnnotationDbi_1.20.6
[12] Biobase_2.18.0
[13] BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] biomaRt_2.14.0     Biostrings_2.26.3  bitops_1.0-5       BSgenome_1.26.1
[5] graph_1.36.2       parallel_2.15.1    RBGL_1.34.0        RCurl_1.95-4.1
[9] Rsamtools_1.10.2   rtracklayer_1.18.2 stats4_2.15.1      tools_2.15.1
[13] XML_3.95-0.2       zlibbioc_1.4.0

b) my old session:
> sessionInfo()
R version 2.15.1 (2012-06-22)
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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] TxDb.Mmusculus.UCSC.mm10.knownGene_2.8.0
[2] BiocInstaller_1.8.3
[3] Mus.musculus_1.0.0
[4] TxDb.Mmusculus.UCSC.mm10.ensGene_2.8.0
[5] org.Mm.eg.db_2.8.0
[6] GO.db_2.8.0
[7] RSQLite_0.11.2
[8] DBI_0.2-5
[9] OrganismDbi_1.0.3
[10] TxDb.Mmusculus.UCSC.mm9.knownGene_2.8.0
[11] GenomicFeatures_1.10.2
[12] AnnotationDbi_1.20.6
[13] Biobase_2.18.0
[14] Rsamtools_1.10.2
[15] Biostrings_2.26.3
[16] TransView_1.0.7
[17] Repitools_1.4.2
[18] GenomicRanges_1.10.7
[19] IRanges_1.16.6
[20] BiocGenerics_0.4.0
[21] ggbio_1.6.6
[22] ggplot2_0.9.3.1

loaded via a namespace (and not attached):
[1] biomaRt_2.14.0           biovizBase_1.6.2         bitops_1.0-5
[4] BSgenome_1.26.1          cluster_1.14.3           colorspace_1.2-1
[7] dichromat_2.0-0          digest_0.6.3             edgeR_3.0.8
[10] gdata_2.12.0             gplots_2.11.0            graph_1.36.2
[13] grid_2.15.1              gridExtra_0.9.1          gtable_0.1.2
[16] gtools_2.7.0             Hmisc_3.10-1             labeling_0.1
[19] lattice_0.20-13          limma_3.14.4             MASS_7.3-23
[22] munsell_0.4              parallel_2.15.1          plyr_1.8
[25] proto_0.3-10             RBGL_1.34.0              RColorBrewer_1.0-5
[28] RCurl_1.95-4.1           reshape2_1.2.2           rtracklayer_1.18.2
[31] scales_0.2.3             stats4_2.15.1            stringr_0.6.2
[34] tools_2.15.1             VariantAnnotation_1.4.12 XML_3.95-0.2
[37] zlibbioc_1.4.0


On Apr 2, 2013, at 3:49 PM, James W. MacDonald wrote:

> 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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