Genominator problem
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Johnny H ▴ 80
@johnny-h-3952
Last seen 8.7 years ago
United Kingdom
Dear Bioconductors, I am using the Genominator library and work through the example...until I get to here > yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id = "ensembl_gene_id", transcript.id = "ensembl_transcript_id", verbose = TRUE) Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'makeUIgenes' not found Please can you advise me how I can use the makeUIgenes method? Subsequent steps in the example don't work without this step. Thank you. > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.8.1 RCurl_1.4-3 bitops_1.0-4.1 Genominator_1.2.0 GenomeGraphs_1.8.0 biomaRt_2.4.0 RSQLite_0.9-2 DBI_0.2-5 ShortRead_1.6.2 Rsamtools_1.0.8 lattice_0.18-8 [12] Biostrings_2.16.9 GenomicRanges_1.0.8 IRanges_1.6.15 yeastRNASeq_0.0.3 loaded via a namespace (and not attached): [1] Biobase_2.8.0 BSgenome_1.16.5 hwriter_1.2 tools_2.11.1 XML_3.1-1 [[alternative HTML version deleted]]
Genominator Genominator • 1.1k views
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@kasper-daniel-hansen-2979
Last seen 9 months ago
United States
This function has been replaced by the more general makeGeneRepresentation. So the call would now be yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") (there are arguments that allow you to set the gene.id and transcript.id but the defaults are set as below). Kasper On Fri, Aug 27, 2010 at 9:48 AM, Johnny H <ukfriend22 at="" googlemail.com=""> wrote: > Dear Bioconductors, > I am using the Genominator library and work through the example...until I > get to here > >> yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id = "ensembl_gene_id", > transcript.id = "ensembl_transcript_id", verbose = TRUE) > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : > ?object 'makeUIgenes' not found > > Please can you advise me how I can use the makeUIgenes method? Subsequent > steps in the example don't work without this step. > > Thank you. > >> sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > locale: > [1] LC_COLLATE=English_United Kingdom.1252 ?LC_CTYPE=English_United > Kingdom.1252 ? ?LC_MONETARY=English_United Kingdom.1252 > LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? ?LC_TIME=English_United > Kingdom.1252 > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > base > other attached packages: > ?[1] rtracklayer_1.8.1 ? RCurl_1.4-3 ? ? ? ? bitops_1.0-4.1 > Genominator_1.2.0 ? GenomeGraphs_1.8.0 ?biomaRt_2.4.0 > RSQLite_0.9-2 ? ? ? DBI_0.2-5 ? ? ? ? ? ShortRead_1.6.2 > Rsamtools_1.0.8 ? ? lattice_0.18-8 > [12] Biostrings_2.16.9 ? GenomicRanges_1.0.8 IRanges_1.6.15 > yeastRNASeq_0.0.3 > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 ? BSgenome_1.16.5 hwriter_1.2 ? ? tools_2.11.1 > XML_3.1-1 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thanks Kasper for that, the command works but... > yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") Error: transcript.id %in% names(annoData) is not TRUE > annoData Error: object 'annoData' not found Where is annoData coming from? On Fri, Aug 27, 2010 at 2:59 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > This function has been replaced by the more general > makeGeneRepresentation. So the call would now be > > yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") > > (there are arguments that allow you to set the gene.id and > transcript.id but the defaults are set as below). > > Kasper > > On Fri, Aug 27, 2010 at 9:48 AM, Johnny H <ukfriend22@googlemail.com> > wrote: > > Dear Bioconductors, > > I am using the Genominator library and work through the example...until I > > get to here > > > >> yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id = > "ensembl_gene_id", > > transcript.id = "ensembl_transcript_id", verbose = TRUE) > > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : > > object 'makeUIgenes' not found > > > > Please can you advise me how I can use the makeUIgenes method? Subsequent > > steps in the example don't work without this step. > > > > Thank you. > > > >> sessionInfo() > > R version 2.11.1 (2010-05-31) > > i386-pc-mingw32 > > locale: > > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > > LC_NUMERIC=C LC_TIME=English_United > > Kingdom.1252 > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > base > > other attached packages: > > [1] rtracklayer_1.8.1 RCurl_1.4-3 bitops_1.0-4.1 > > Genominator_1.2.0 GenomeGraphs_1.8.0 biomaRt_2.4.0 > > RSQLite_0.9-2 DBI_0.2-5 ShortRead_1.6.2 > > Rsamtools_1.0.8 lattice_0.18-8 > > [12] Biostrings_2.16.9 GenomicRanges_1.0.8 IRanges_1.6.15 > > yeastRNASeq_0.0.3 > > loaded via a namespace (and not attached): > > [1] Biobase_2.8.0 BSgenome_1.16.5 hwriter_1.2 tools_2.11.1 > > XML_3.1-1 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]
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Inside the function, annoData is just the yAnno data.frame. The error means that transcript.id - with a default value of "ensembl_transcript_id" is not part of the names (colnames) of the yAnno object. At this time you should show us head(yAnno) and tell us exactly what document you are following. Kasper On Fri, Aug 27, 2010 at 10:03 AM, Johnny H <ukfriend22 at="" googlemail.com=""> wrote: > Thanks Kasper for that, the command works but... > >> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") > Error: transcript.id %in% names(annoData) is not TRUE >> annoData > Error: object 'annoData' not found > Where is annoData coming from? > > On Fri, Aug 27, 2010 at 2:59 PM, Kasper Daniel Hansen > <kasperdanielhansen at="" gmail.com=""> wrote: >> >> This function has been replaced by the more general >> makeGeneRepresentation. ?So the call would now be >> >> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") >> >> (there are arguments that allow you to set the gene.id and >> transcript.id but the defaults are set as below). >> >> Kasper >> >> On Fri, Aug 27, 2010 at 9:48 AM, Johnny H <ukfriend22 at="" googlemail.com=""> >> wrote: >> > Dear Bioconductors, >> > I am using the Genominator library and work through the example...until >> > I >> > get to here >> > >> >> yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id = >> >> "ensembl_gene_id", >> > transcript.id = "ensembl_transcript_id", verbose = TRUE) >> > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : >> > ?object 'makeUIgenes' not found >> > >> > Please can you advise me how I can use the makeUIgenes method? >> > Subsequent >> > steps in the example don't work without this step. >> > >> > Thank you. >> > >> >> sessionInfo() >> > R version 2.11.1 (2010-05-31) >> > i386-pc-mingw32 >> > locale: >> > [1] LC_COLLATE=English_United Kingdom.1252 ?LC_CTYPE=English_United >> > Kingdom.1252 ? ?LC_MONETARY=English_United Kingdom.1252 >> > LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? ?LC_TIME=English_United >> > Kingdom.1252 >> > attached base packages: >> > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods >> > base >> > other attached packages: >> > ?[1] rtracklayer_1.8.1 ? RCurl_1.4-3 ? ? ? ? bitops_1.0-4.1 >> > Genominator_1.2.0 ? GenomeGraphs_1.8.0 ?biomaRt_2.4.0 >> > RSQLite_0.9-2 ? ? ? DBI_0.2-5 ? ? ? ? ? ShortRead_1.6.2 >> > Rsamtools_1.0.8 ? ? lattice_0.18-8 >> > [12] Biostrings_2.16.9 ? GenomicRanges_1.0.8 IRanges_1.6.15 >> > yeastRNASeq_0.0.3 >> > loaded via a namespace (and not attached): >> > [1] Biobase_2.8.0 ? BSgenome_1.16.5 hwriter_1.2 ? ? tools_2.11.1 >> > XML_3.1-1 >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > >
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