[BioC] known gene => gene symbol for UCSC
James W. MacDonald
jmacdon at uw.edu
Tue Apr 2 17:01:58 CEST 2013
Hi Ido,
On 4/2/2013 10:20 AM, Ido Tamir wrote:
> 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.
Fair enough. However, the new release is upon us and this has evidently
been fixed in the new version. So if I were you, I would upgrade to
R-3.0.0 and BioC-2.12
Best,
Jim
> 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
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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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
>>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
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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