BUG in Genomic(Features|Ranges): names(unlist(transcriptsBy(txdb, 'gene'))) is UNRELIABLE!!!
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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 22 hours ago
United States
Careful fellow travelers, I find that unlisting the GenomicRanges returned from a call to `transcriptsBy` returns a list with names that are gene names... only they are incorrect! Look: > txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl") ... > transcriptsBy(txdb,'gene')[2] GRangesList of length 1: $FBgn0000008 GRanges with 3 ranges and 2 elementMetadata cols: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] 2R [18024494, 18060339] + | 8616 FBtr0100521 [2] 2R [18024496, 18060346] + | 8615 FBtr0071763 [3] 2R [18024938, 18060346] + | 8617 FBtr0071764 ... > unlist(transcriptsBy(txdb,'gene')[2]) GRanges with 3 ranges and 2 elementMetadata cols: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> FBgn0000008 2R [18024494, 18060339] + | 8616 FBtr0100521 FBgn00000081 2R [18024496, 18060346] + | 8615 FBtr0071763 FBgn00000082 2R [18024938, 18060346] + | 8617 FBtr0071764 ... Arguably, those names on the the GRanges should either all be the same, namely FBgn0000008, or they should not be returned. This 'bug' has been around for a some time. I meant to report it, and just tripped over it again. Can fix? Thanks! Malcolm > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools splines parallel stats graphics grDevices utils datasets methods base other attached packages: [1] igraph_0.6-2 log4r_0.1-4 vwr_0.1 RecordLinkage_0.4-1 ffbase_0.5 ff_2.2-7 bit_1.1-8 evd_2.2-7 ipred_0.8-13 prodlim_1.3.1 KernSmooth_2.23-8 nnet_7.3-4 survival_2.36-14 mlbench_2.1-1 MASS_7.3-20 ada_2.0-3 rpart_3.1-54 e1071_1.6 class_7.3-4 XLConnect_0.2-0 XLConnectJars_0.2-0 rJava_0.9-3 latticeExtra_0.6-19 RColorBrewer_1.0-5 lattice_0.20-6 doMC_1.2.5 multicore_0.1-7 [28] SRAdb_1.10.0 RCurl_1.91-1 bitops_1.0-4.1 graph_1.34.0 BSgenome_1.24.0 rtracklayer_1.16.3 Rsamtools_1.8.6 Biostrings_2.24.1 GenomicFeatures_1.8.2 AnnotationDbi_1.19.31 GenomicRanges_1.8.12 R.utils_1.16.0 R.oo_1.9.8 R.methodsS3_1.4.2 IRanges_1.14.4 Biobase_2.17.7 BiocGenerics_0.3.1 data.table_1.8.2 compare_0.2-3 svUnit_0.7-10 doParallel_1.0.1 iterators_1.0.6 foreach_1.4.0 ggplot2_0.9.1 sqldf_0.4-6.4 RSQLite.extfuns_0.0.1 RSQLite_0.11.1 [55] chron_2.3-42 gsubfn_0.6-4 proto_0.3-9.2 DBI_0.2-5 functional_0.1 reshape_0.8.4 plyr_1.7.1 stringr_0.6.1 gtools_2.7.0 loaded via a namespace (and not attached): [1] biomaRt_2.12.0 codetools_0.2-8 colorspace_1.1-1 compiler_2.15.0 dichromat_1.2-4 digest_0.5.2 GEOquery_2.23.5 grid_2.15.0 labeling_0.1 memoise_0.1 munsell_0.3 reshape2_1.2.1 scales_0.2.1 stats4_2.15.0 tcltk_2.15.0 XML_3.9-4 zlibbioc_1.2.0 >
GenomicRanges GenomicRanges • 846 views
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@martin-morgan-1513
Last seen 16 days ago
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On 08/31/2012 10:07 PM, Cook, Malcolm wrote: > Careful fellow travelers, > > I find that unlisting the GenomicRanges returned from a call to `transcriptsBy` returns a list with names that are gene names... only they are incorrect! > > Look: > >> txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl") > ... >> transcriptsBy(txdb,'gene')[2] > GRangesList of length 1: > $FBgn0000008 > GRanges with 3 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] 2R [18024494, 18060339] + | 8616 FBtr0100521 > [2] 2R [18024496, 18060346] + | 8615 FBtr0071763 > [3] 2R [18024938, 18060346] + | 8617 FBtr0071764 > ... >> unlist(transcriptsBy(txdb,'gene')[2]) > GRanges with 3 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > FBgn0000008 2R [18024494, 18060339] + | 8616 FBtr0100521 > FBgn00000081 2R [18024496, 18060346] + | 8615 FBtr0071763 > FBgn00000082 2R [18024938, 18060346] + | 8617 FBtr0071764 > ... > > > Arguably, those names on the the GRanges should either all be the same, namely FBgn0000008, or they should not be returned. This is the way unlist works in base R > unlist(list(a=1:2)) a1 a2 1 2 but the behavior has been changed in devel (to be release in early October) > unlist(GRangesList(A=GRanges("a", IRanges(1:2, 10)))) GRanges with 2 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> A a [1, 10] * A a [2, 10] * --- seqlengths: a NA the work-around, as in base R, is to add use.names=FALSE to unlist (perhaps adding a metadata column of rep(names(txdb), elementLengths(txdb))). > This 'bug' has been around for a some time. I meant to report it, and just tripped over it again. > > Can fix? > > Thanks! > > Malcolm > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools splines parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] igraph_0.6-2 log4r_0.1-4 vwr_0.1 RecordLinkage_0.4-1 ffbase_0.5 ff_2.2-7 bit_1.1-8 evd_2.2-7 ipred_0.8-13 prodlim_1.3.1 KernSmooth_2.23-8 nnet_7.3-4 survival_2.36-14 mlbench_2.1-1 MASS_7.3-20 ada_2.0-3 rpart_3.1-54 e1071_1.6 class_7.3-4 XLConnect_0.2-0 XLConnectJars_0.2-0 rJava_0.9-3 latticeExtra_0.6-19 RColorBrewer_1.0-5 lattice_0.20-6 doMC_1.2.5 multicore_0.1-7 > [28] SRAdb_1.10.0 RCurl_1.91-1 bitops_1.0-4.1 graph_1.34.0 BSgenome_1.24.0 rtracklayer_1.16.3 Rsamtools_1.8.6 Biostrings_2.24.1 GenomicFeatures_1.8.2 AnnotationDbi_1.19.31 GenomicRanges_1.8.12 R.utils_1.16.0 R.oo_1.9.8 R.methodsS3_1.4.2 IRanges_1.14.4 Biobase_2.17.7 BiocGenerics_0.3.1 data.table_1.8.2 compare_0.2-3 svUnit_0.7-10 doParallel_1.0.1 iterators_1.0.6 foreach_1.4.0 ggplot2_0.9.1 sqldf_0.4-6.4 RSQLite.extfuns_0.0.1 RSQLite_0.11.1 > [55] chron_2.3-42 gsubfn_0.6-4 proto_0.3-9.2 DBI_0.2-5 functional_0.1 reshape_0.8.4 plyr_1.7.1 stringr_0.6.1 gtools_2.7.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.12.0 codetools_0.2-8 colorspace_1.1-1 compiler_2.15.0 dichromat_1.2-4 digest_0.5.2 GEOquery_2.23.5 grid_2.15.0 labeling_0.1 memoise_0.1 munsell_0.3 reshape2_1.2.1 scales_0.2.1 stats4_2.15.0 tcltk_2.15.0 XML_3.9-4 zlibbioc_1.2.0 >> -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hmm, I was about to say "that's not the way it works in devel!!" but there you go. More generally, I wonder if this couldn't be fixed once and for all: Unlist can be maddening -- I would like to add a version (perhaps to BiocGenerics) that uses a .[1:length(x)] extension instead of the current default of pasting c('', 1:(length(x)-1)) to the name. Personally it seems like this would actually better overall as a default, even in base R. Perhaps I ought to bring up this notion? Any reason not to risk the ire of Professor Ripley again? Worst case, he points out why this is an idiotic idea and I learn something in the process. thanks, --t On Sat, Sep 1, 2012 at 6:35 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 08/31/2012 10:07 PM, Cook, Malcolm wrote: > >> Careful fellow travelers, >> >> I find that unlisting the GenomicRanges returned from a call to >> `transcriptsBy` returns a list with names that are gene names... only they >> are incorrect! >> >> Look: >> >> txdb<-**makeTranscriptDbFromBiomart(**biomart="ensembl", >>> dataset="dmelanogaster_gene_**ensembl") >>> >> ... >> >>> transcriptsBy(txdb,'gene')[2] >>> >> GRangesList of length 1: >> $FBgn0000008 >> GRanges with 3 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id tx_name >> <rle> <iranges> <rle> | <integer> <character> >> [1] 2R [18024494, 18060339] + | 8616 FBtr0100521 >> [2] 2R [18024496, 18060346] + | 8615 FBtr0071763 >> [3] 2R [18024938, 18060346] + | 8617 FBtr0071764 >> ... >> >>> unlist(transcriptsBy(txdb,'**gene')[2]) >>> >> GRanges with 3 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id >> tx_name >> <rle> <iranges> <rle> | <integer> >> <character> >> FBgn0000008 2R [18024494, 18060339] + | 8616 >> FBtr0100521 >> FBgn00000081 2R [18024496, 18060346] + | 8615 >> FBtr0071763 >> FBgn00000082 2R [18024938, 18060346] + | 8617 >> FBtr0071764 >> ... >> >> >> Arguably, those names on the the GRanges should either all be the same, >> namely FBgn0000008, or they should not be returned. >> > > This is the way unlist works in base R > > > unlist(list(a=1:2)) > a1 a2 > 1 2 > > but the behavior has been changed in devel (to be release in early October) > > > unlist(GRangesList(A=GRanges("**a", IRanges(1:2, 10)))) > GRanges with 2 ranges and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > A a [1, 10] * > A a [2, 10] * > --- > seqlengths: > a > NA > > the work-around, as in base R, is to add use.names=FALSE to unlist > (perhaps adding a metadata column of rep(names(txdb), > elementLengths(txdb))). > > > This 'bug' has been around for a some time. I meant to report it, and >> just tripped over it again. >> >> Can fix? >> >> Thanks! >> >> Malcolm >> >> sessionInfo() >>> >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8 >> >> attached base packages: >> [1] tools splines parallel stats graphics grDevices utils >> datasets methods base >> >> other attached packages: >> [1] igraph_0.6-2 log4r_0.1-4 vwr_0.1 >> RecordLinkage_0.4-1 ffbase_0.5 ff_2.2-7 bit_1.1-8 >> evd_2.2-7 ipred_0.8-13 prodlim_1.3.1 >> KernSmooth_2.23-8 nnet_7.3-4 survival_2.36-14 >> mlbench_2.1-1 MASS_7.3-20 ada_2.0-3 >> rpart_3.1-54 e1071_1.6 class_7.3-4 >> XLConnect_0.2-0 XLConnectJars_0.2-0 rJava_0.9-3 >> latticeExtra_0.6-19 RColorBrewer_1.0-5 lattice_0.20-6 >> doMC_1.2.5 multicore_0.1-7 >> [28] SRAdb_1.10.0 RCurl_1.91-1 bitops_1.0-4.1 >> graph_1.34.0 BSgenome_1.24.0 rtracklayer_1.16.3 >> Rsamtools_1.8.6 Biostrings_2.24.1 GenomicFeatures_1.8.2 >> AnnotationDbi_1.19.31 GenomicRanges_1.8.12 R.utils_1.16.0 >> R.oo_1.9.8 R.methodsS3_1.4.2 IRanges_1.14.4 >> Biobase_2.17.7 BiocGenerics_0.3.1 data.table_1.8.2 >> compare_0.2-3 svUnit_0.7-10 doParallel_1.0.1 >> iterators_1.0.6 foreach_1.4.0 ggplot2_0.9.1 >> sqldf_0.4-6.4 RSQLite.extfuns_0.0.1 RSQLite_0.11.1 >> [55] chron_2.3-42 gsubfn_0.6-4 proto_0.3-9.2 >> DBI_0.2-5 functional_0.1 reshape_0.8.4 >> plyr_1.7.1 stringr_0.6.1 gtools_2.7.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.12.0 codetools_0.2-8 colorspace_1.1-1 compiler_2.15.0 >> dichromat_1.2-4 digest_0.5.2 GEOquery_2.23.5 grid_2.15.0 >> labeling_0.1 memoise_0.1 munsell_0.3 reshape2_1.2.1 >> scales_0.2.1 stats4_2.15.0 tcltk_2.15.0 XML_3.9-4 >> zlibbioc_1.2.0 >> >>> >>> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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On 09/01/2012 12:24 PM, Tim Triche, Jr. wrote: > Hmm, I was about to say "that's not the way it works in devel!!" but > there you go. More generally, I wonder if this couldn't be fixed once > and for all: > > Unlist can be maddening -- I would like to add a version (perhaps to > BiocGenerics) that uses a .[1:length(x)] extension instead of the > current default of pasting c('', 1:(length(x)-1)) to the name. > Personally it seems like this would actually better overall as a > default, even in base R. Perhaps I ought to bring up this notion? BiocGenerics tries not to mess with function signatures; it's used widely and so wants to play as nicely as possible with other packages. Martin > Any reason not to risk the ire of Professor Ripley again? Worst case, > he points out why this is an idiotic idea and I learn something in the > process. > > thanks, > > --t > > > > On Sat, Sep 1, 2012 at 6:35 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 08/31/2012 10:07 PM, Cook, Malcolm wrote: > > Careful fellow travelers, > > I find that unlisting the GenomicRanges returned from a call to > `transcriptsBy` returns a list with names that are gene names... > only they are incorrect! > > Look: > > txdb<-__makeTranscriptDbFromBiomart(__biomart="ensembl", > dataset="dmelanogaster_gene___ensembl") > > ... > > transcriptsBy(txdb,'gene')[2] > > GRangesList of length 1: > $FBgn0000008 > GRanges with 3 ranges and 2 elementMetadata cols: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] 2R [18024494, 18060339] + | 8616 FBtr0100521 > [2] 2R [18024496, 18060346] + | 8615 FBtr0071763 > [3] 2R [18024938, 18060346] + | 8617 FBtr0071764 > ... > > unlist(transcriptsBy(txdb,'__gene')[2]) > > GRanges with 3 ranges and 2 elementMetadata cols: > seqnames ranges strand | > tx_id tx_name > <rle> <iranges> <rle> | > <integer> <character> > FBgn0000008 2R [18024494, 18060339] + | > 8616 FBtr0100521 > FBgn00000081 2R [18024496, 18060346] + | > 8615 FBtr0071763 > FBgn00000082 2R [18024938, 18060346] + | > 8617 FBtr0071764 > ... > > > Arguably, those names on the the GRanges should either all be > the same, namely FBgn0000008, or they should not be returned. > > > This is the way unlist works in base R > > > unlist(list(a=1:2)) > a1 a2 > 1 2 > > but the behavior has been changed in devel (to be release in early > October) > > > unlist(GRangesList(A=GRanges("__a", IRanges(1:2, 10)))) > GRanges with 2 ranges and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > A a [1, 10] * > A a [2, 10] * > --- > seqlengths: > a > NA > > the work-around, as in base R, is to add use.names=FALSE to unlist > (perhaps adding a metadata column of rep(names(txdb), > elementLengths(txdb))). > > > This 'bug' has been around for a some time. I meant to report > it, and just tripped over it again. > > Can fix? > > Thanks! > > Malcolm > > sessionInfo() > > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86___64 (64-bit) > > locale: > [1] > en_US.UTF-8/en_US.UTF-8/en_US.__UTF-8/C/en_US.UTF-8/en_US .UTF-__8 > > attached base packages: > [1] tools splines parallel stats graphics > grDevices utils datasets methods base > > other attached packages: > [1] igraph_0.6-2 log4r_0.1-4 vwr_0.1 > RecordLinkage_0.4-1 ffbase_0.5 ff_2.2-7 > bit_1.1-8 evd_2.2-7 > ipred_0.8-13 prodlim_1.3.1 KernSmooth_2.23-8 > nnet_7.3-4 survival_2.36-14 mlbench_2.1-1 > MASS_7.3-20 ada_2.0-3 rpart_3.1-54 > e1071_1.6 class_7.3-4 > XLConnect_0.2-0 XLConnectJars_0.2-0 rJava_0.9-3 > latticeExtra_0.6-19 RColorBrewer_1.0-5 lattice_0.20-6 > doMC_1.2.5 multicore_0.1-7 > [28] SRAdb_1.10.0 RCurl_1.91-1 bitops_1.0-4.1 > graph_1.34.0 BSgenome_1.24.0 > rtracklayer_1.16.3 Rsamtools_1.8.6 Biostrings_2.24.1 > GenomicFeatures_1.8.2 AnnotationDbi_1.19.31 > GenomicRanges_1.8.12 R.utils_1.16.0 R.oo_1.9.8 > R.methodsS3_1.4.2 IRanges_1.14.4 Biobase_2.17.7 > BiocGenerics_0.3.1 data.table_1.8.2 compare_0.2-3 > svUnit_0.7-10 doParallel_1.0.1 > iterators_1.0.6 foreach_1.4.0 ggplot2_0.9.1 > sqldf_0.4-6.4 RSQLite.extfuns_0.0.1 RSQLite_0.11.1 > [55] chron_2.3-42 gsubfn_0.6-4 proto_0.3-9.2 > DBI_0.2-5 functional_0.1 reshape_0.8.4 > plyr_1.7.1 stringr_0.6.1 gtools_2.7.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.12.0 codetools_0.2-8 colorspace_1.1-1 > compiler_2.15.0 dichromat_1.2-4 digest_0.5.2 > GEOquery_2.23.5 grid_2.15.0 labeling_0.1 memoise_0.1 > munsell_0.3 reshape2_1.2.1 scales_0.2.1 > stats4_2.15.0 tcltk_2.15.0 XML_3.9-4 zlibbioc_1.2.0 > > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 <tel:%28206%29%20667-2793> > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > -- > /A model is a lie that helps you see the truth./ > / > / > Howard Skipper > <http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Martin, Ah, so sorry. The BUG is in my understanding of base R. Thanks for your time to fix my thinking. Gracias, Malcolm On 9/1/12 8:35 AM, "Martin Morgan" <mtmorgan at="" fhcrc.org=""> wrote: >On 08/31/2012 10:07 PM, Cook, Malcolm wrote: >> Careful fellow travelers, >> >> I find that unlisting the GenomicRanges returned from a call to >>`transcriptsBy` returns a list with names that are gene names... only >>they are incorrect! >> >> Look: >> >>> txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", >>>dataset="dmelanogaster_gene_ensembl") >> ... >>> transcriptsBy(txdb,'gene')[2] >> GRangesList of length 1: >> $FBgn0000008 >> GRanges with 3 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id tx_name >> <rle> <iranges> <rle> | <integer> <character> >> [1] 2R [18024494, 18060339] + | 8616 FBtr0100521 >> [2] 2R [18024496, 18060346] + | 8615 FBtr0071763 >> [3] 2R [18024938, 18060346] + | 8617 FBtr0071764 >> ... >>> unlist(transcriptsBy(txdb,'gene')[2]) >> GRanges with 3 ranges and 2 elementMetadata cols: >> seqnames ranges strand | tx_id >>tx_name >> <rle> <iranges> <rle> | <integer> >><character> >> FBgn0000008 2R [18024494, 18060339] + | 8616 >>FBtr0100521 >> FBgn00000081 2R [18024496, 18060346] + | 8615 >>FBtr0071763 >> FBgn00000082 2R [18024938, 18060346] + | 8617 >>FBtr0071764 >> ... >> >> >> Arguably, those names on the the GRanges should either all be the same, >>namely FBgn0000008, or they should not be returned. > >This is the way unlist works in base R > > > unlist(list(a=1:2)) >a1 a2 > 1 2 > >but the behavior has been changed in devel (to be release in early >October) > > > unlist(GRangesList(A=GRanges("a", IRanges(1:2, 10)))) >GRanges with 2 ranges and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > A a [1, 10] * > A a [2, 10] * > --- > seqlengths: > a > NA > >the work-around, as in base R, is to add use.names=FALSE to unlist >(perhaps adding a metadata column of rep(names(txdb), >elementLengths(txdb))). > >> This 'bug' has been around for a some time. I meant to report it, and >>just tripped over it again. >> >> Can fix? >> >> Thanks! >> >> Malcolm >> >>> sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] tools splines parallel stats graphics grDevices utils >> datasets methods base >> >> other attached packages: >> [1] igraph_0.6-2 log4r_0.1-4 vwr_0.1 >>RecordLinkage_0.4-1 ffbase_0.5 ff_2.2-7 >>bit_1.1-8 evd_2.2-7 ipred_0.8-13 >>prodlim_1.3.1 KernSmooth_2.23-8 nnet_7.3-4 >>survival_2.36-14 mlbench_2.1-1 MASS_7.3-20 >>ada_2.0-3 rpart_3.1-54 e1071_1.6 >>class_7.3-4 XLConnect_0.2-0 XLConnectJars_0.2-0 >>rJava_0.9-3 latticeExtra_0.6-19 RColorBrewer_1.0-5 >>lattice_0.20-6 doMC_1.2.5 multicore_0.1-7 >> [28] SRAdb_1.10.0 RCurl_1.91-1 bitops_1.0-4.1 >>graph_1.34.0 BSgenome_1.24.0 rtracklayer_1.16.3 >>Rsamtools_1.8.6 Biostrings_2.24.1 GenomicFeatures_1.8.2 >>AnnotationDbi_1.19.31 GenomicRanges_1.8.12 R.utils_1.16.0 >>R.oo_1.9.8 R.methodsS3_1.4.2 IRanges_1.14.4 >>Biobase_2.17.7 BiocGenerics_0.3.1 data.table_1.8.2 >>compare_0.2-3 svUnit_0.7-10 doParallel_1.0.1 >>iterators_1.0.6 foreach_1.4.0 ggplot2_0.9.1 >>sqldf_0.4-6.4 RSQLite.extfuns_0.0.1 RSQLite_0.11.1 >> [55] chron_2.3-42 gsubfn_0.6-4 proto_0.3-9.2 >>DBI_0.2-5 functional_0.1 reshape_0.8.4 >>plyr_1.7.1 stringr_0.6.1 gtools_2.7.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.12.0 codetools_0.2-8 colorspace_1.1-1 >>compiler_2.15.0 dichromat_1.2-4 digest_0.5.2 GEOquery_2.23.5 >>grid_2.15.0 labeling_0.1 memoise_0.1 munsell_0.3 >>reshape2_1.2.1 scales_0.2.1 stats4_2.15.0 tcltk_2.15.0 >>XML_3.9-4 zlibbioc_1.2.0 >>> > > >-- >Computational Biology / Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. >PO Box 19024 Seattle, WA 98109 > >Location: Arnold Building M1 B861 >Phone: (206) 667-2793
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