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 >>> 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 >> > _______________________________________________ > 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