Hi, I am using findOverlaps() to compare two GRanges objects (shown below). ensembl.genes was created with rtracklayer import.gff(...,genome="hg19"), so it contains additional information about the genome. exons was created manually from a list of positions etc. It seems that I can no longer compare the two objects which previously worked fine (I am not sure whether I already used this script on R-devel, but it definitely worked on R-2.13). I would be happy for any suggestions how to overcome this problem. Thanks for your help, Kathi > findOverlaps(ensembl.genes,exons) Error in genome(y) : no slot of name "genome" for this object of class "Seqinfo" > head(exons) GRanges with 6 ranges and 7 elementMetadata values: seqnames ranges strand | phase section.id <rle> <iranges> <rle> | <numeric> <character> [1] chr1 [ 704549, 704591] - | 1 CUFF.1135:003 [2] chr1 [ 764383, 764484] + | 0 CUFF.825:003 [3] chr1 [1654546, 1654661] - | 2 CUFF.6345:097 [4] chr1 [2303220, 2303344] - | 2 CUFF.5141:008 [5] chr1 [3776984, 3777005] + | 1 CUFF.2849:006 [6] chr1 [6297305, 6297405] + | 2 CUFF.3421:002 exon.position splice.3 splice.5 ensembl.overlap ensg <character> <logical> <logical> <character> <logical> [1] terminal TRUE FALSE novel <na> [2] internal TRUE TRUE any_overlap <na> [3] terminal FALSE TRUE novel <na> [4] internal TRUE FALSE any_overlap <na> [5] terminal TRUE FALSE any_overlap <na> [6] internal TRUE TRUE any_overlap <na> --- seqlengths: chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX chrY NA NA NA NA NA NA ... NA NA NA NA NA NA > head(ensembl.genes) GRanges with 6 ranges and 1 elementMetadata value: seqnames ranges strand | ensg <rle> <iranges> <rle> | <character> [1] chrX [ 99883667, 99894988] - | ENSG00000000003 [2] chrX [ 99839799, 99854882] + | ENSG00000000005 [3] chr20 [ 49551404, 49575092] - | ENSG00000000419 [4] chr1 [169821804, 169863408] - | ENSG00000000457 [5] chr1 [169631245, 169823221] + | ENSG00000000460 [6] chr1 [ 27938575, 27961788] - | ENSG00000000938 --- seqlengths: chr1 chr10 ... chrY NA NA ... NA > sessionInfo() R Under development (unstable) (2011-08-14 r56741) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DEXSeq_0.1.29 Biobase_2.13.10 biomaRt_2.9.3 [4] xtable_1.5-6 GenomicRanges_1.5.49 IRanges_1.11.30 [7] R.utils_1.8.2 R.oo_1.8.2 R.methodsS3_1.2.1 [10] rtracklayer_1.13.17 RCurl_1.6-10 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biostrings_2.21.11 BSgenome_1.21.6 hwriter_1.3 MASS_7.3-14 [5] plyr_1.6 stringr_0.5 tools_2.14.0 XML_3.4-3 [9] zlibbioc_0.1.8 > -- Dr. Kathi Zarnack Luscombe Group European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK tel +44 1223 494 526

ensembl.genes <- IRanges::updateObject(ensembl.genes) exons <- IRanges::updateObject(exons) And save those. Btw, you should really get the ensembl.gene information using GenomicFeatures, using makeTranscriptDbFromUCSC and going for the ensGene table. On Fri, Oct 21, 2011 at 4:50 AM, Kathi Zarnack <zarnack@ebi.ac.uk> wrote: > Hi, > > I am using findOverlaps() to compare two GRanges objects (shown below). > ensembl.genes was created with rtracklayer import.gff(...,genome="hg19"), so > it contains additional information about the genome. exons was created > manually from a list of positions etc. It seems that I can no longer compare > the two objects which previously worked fine (I am not sure whether I > already used this script on R-devel, but it definitely worked on R-2.13). I > would be happy for any suggestions how to overcome this problem. > > Thanks for your help, > Kathi > > > findOverlaps(ensembl.genes,**exons) > Error in genome(y) : > no slot of name "genome" for this object of class "Seqinfo" > > > head(exons) > GRanges with 6 ranges and 7 elementMetadata values: > seqnames ranges strand | phase section.id > <rle> <iranges> <rle> | <numeric> <character> > [1] chr1 [ 704549, 704591] - | 1 CUFF.1135:003 > [2] chr1 [ 764383, 764484] + | 0 CUFF.825:003 > [3] chr1 [1654546, 1654661] - | 2 CUFF.6345:097 > [4] chr1 [2303220, 2303344] - | 2 CUFF.5141:008 > [5] chr1 [3776984, 3777005] + | 1 CUFF.2849:006 > [6] chr1 [6297305, 6297405] + | 2 CUFF.3421:002 > exon.position splice.3 splice.5 ensembl.overlap ensg > <character> <logical> <logical> <character> <logical> > [1] terminal TRUE FALSE novel <na> > [2] internal TRUE TRUE any_overlap <na> > [3] terminal FALSE TRUE novel <na> > [4] internal TRUE FALSE any_overlap <na> > [5] terminal TRUE FALSE any_overlap <na> > [6] internal TRUE TRUE any_overlap <na> > --- > seqlengths: > chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX > chrY > NA NA NA NA NA NA ... NA NA NA NA NA > NA > > > head(ensembl.genes) > GRanges with 6 ranges and 1 elementMetadata value: > seqnames ranges strand | ensg > <rle> <iranges> <rle> | <character> > [1] chrX [ 99883667, 99894988] - | ENSG00000000003 > [2] chrX [ 99839799, 99854882] + | ENSG00000000005 > [3] chr20 [ 49551404, 49575092] - | ENSG00000000419 > [4] chr1 [169821804, 169863408] - | ENSG00000000457 > [5] chr1 [169631245, 169823221] + | ENSG00000000460 > [6] chr1 [ 27938575, 27961788] - | ENSG00000000938 > --- > seqlengths: > chr1 chr10 ... chrY > NA NA ... NA > > > sessionInfo() > R Under development (unstable) (2011-08-14 r56741) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DEXSeq_0.1.29 Biobase_2.13.10 biomaRt_2.9.3 > [4] xtable_1.5-6 GenomicRanges_1.5.49 IRanges_1.11.30 > [7] R.utils_1.8.2 R.oo_1.8.2 R.methodsS3_1.2.1 > [10] rtracklayer_1.13.17 RCurl_1.6-10 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.21.11 BSgenome_1.21.6 hwriter_1.3 MASS_7.3-14 > [5] plyr_1.6 stringr_0.5 tools_2.14.0 XML_3.4-3 > [9] zlibbioc_0.1.8 > > > > -- > Dr. Kathi Zarnack > Luscombe Group > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD, UK > tel +44 1223 494 526 > > ______________________________**_________________ > 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=""> > [[alternative HTML version deleted]]

ensure that you have current package versions and then try updateObject() on the constituents of your call. if that doesn't work let us know. On Fri, Oct 21, 2011 at 7:50 AM, Kathi Zarnack <zarnack at="" ebi.ac.uk=""> wrote: > Hi, > > I am using findOverlaps() to compare two GRanges objects (shown below). > ensembl.genes was created with rtracklayer import.gff(...,genome="hg19"), so > it contains additional information about the genome. exons was created > manually from a list of positions etc. It seems that I can no longer compare > the two objects which previously worked fine (I am not sure whether I > already used this script on R-devel, but it definitely worked on R-2.13). I > would be happy for any suggestions how to overcome this problem. > > Thanks for your help, > Kathi > >> findOverlaps(ensembl.genes,exons) > Error in genome(y) : > ?no slot of name "genome" for this object of class "Seqinfo" > >> head(exons) > GRanges with 6 ranges and 7 elementMetadata values: > ? ? ?seqnames ? ? ? ? ? ? ranges strand | ? ? phase ? ?section.id > <rle> <iranges> <rle> | <numeric> <character> > ?[1] ? ? chr1 [ 704549, ?704591] ? ? ?- | ? ? ? ? 1 CUFF.1135:003 > ?[2] ? ? chr1 [ 764383, ?764484] ? ? ?+ | ? ? ? ? 0 ?CUFF.825:003 > ?[3] ? ? chr1 [1654546, 1654661] ? ? ?- | ? ? ? ? 2 CUFF.6345:097 > ?[4] ? ? chr1 [2303220, 2303344] ? ? ?- | ? ? ? ? 2 CUFF.5141:008 > ?[5] ? ? chr1 [3776984, 3777005] ? ? ?+ | ? ? ? ? 1 CUFF.2849:006 > ?[6] ? ? chr1 [6297305, 6297405] ? ? ?+ | ? ? ? ? 2 CUFF.3421:002 > ? ? ?exon.position ?splice.3 ?splice.5 ensembl.overlap ? ? ?ensg > <character> <logical> <logical> <character> <logical> > ?[1] ? ? ?terminal ? ? ?TRUE ? ? FALSE ? ? ? ? ? novel <na> > ?[2] ? ? ?internal ? ? ?TRUE ? ? ?TRUE ? ? any_overlap <na> > ?[3] ? ? ?terminal ? ? FALSE ? ? ?TRUE ? ? ? ? ? novel <na> > ?[4] ? ? ?internal ? ? ?TRUE ? ? FALSE ? ? any_overlap <na> > ?[5] ? ? ?terminal ? ? ?TRUE ? ? FALSE ? ? any_overlap <na> > ?[6] ? ? ?internal ? ? ?TRUE ? ? ?TRUE ? ? any_overlap <na> > ?--- > ?seqlengths: > ? ?chr1 chr10 chr11 chr12 chr13 chr14 ... ?chr6 ?chr7 ?chr8 ?chr9 ?chrX > ?chrY > ? ? ?NA ? ?NA ? ?NA ? ?NA ? ?NA ? ?NA ... ? ?NA ? ?NA ? ?NA ? ?NA ? ?NA > ?NA > >> head(ensembl.genes) > GRanges with 6 ranges and 1 elementMetadata value: > ? ? ?seqnames ? ? ? ? ? ? ? ? ranges strand | ? ? ? ? ? ?ensg > <rle> <iranges> <rle> | <character> > ?[1] ? ? chrX [ 99883667, ?99894988] ? ? ?- | ENSG00000000003 > ?[2] ? ? chrX [ 99839799, ?99854882] ? ? ?+ | ENSG00000000005 > ?[3] ? ?chr20 [ 49551404, ?49575092] ? ? ?- | ENSG00000000419 > ?[4] ? ? chr1 [169821804, 169863408] ? ? ?- | ENSG00000000457 > ?[5] ? ? chr1 [169631245, 169823221] ? ? ?+ | ENSG00000000460 > ?[6] ? ? chr1 [ 27938575, ?27961788] ? ? ?- | ENSG00000000938 > ?--- > ?seqlengths: > ? ? ? ? ? ? ? ? chr1 ? ? ? ? ? ? ?chr10 ... ? ? ? ? ? ? ? chrY > ? ? ? ? ? ? ? ? ? NA ? ? ? ? ? ? ? ? NA ... ? ? ? ? ? ? ? ? NA > >> sessionInfo() > R Under development (unstable) (2011-08-14 r56741) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_GB.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_GB.UTF-8 ? ? ? ?LC_COLLATE=en_GB.UTF-8 > ?[5] LC_MONETARY=en_GB.UTF-8 ? ?LC_MESSAGES=en_GB.UTF-8 > ?[7] LC_PAPER=C ? ? ? ? ? ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] DEXSeq_0.1.29 ? ? ? ?Biobase_2.13.10 ? ? ?biomaRt_2.9.3 > ?[4] xtable_1.5-6 ? ? ? ? GenomicRanges_1.5.49 IRanges_1.11.30 > ?[7] R.utils_1.8.2 ? ? ? ?R.oo_1.8.2 ? ? ? ? ? R.methodsS3_1.2.1 > [10] rtracklayer_1.13.17 ?RCurl_1.6-10 ? ? ? ? bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.21.11 BSgenome_1.21.6 ? ?hwriter_1.3 ? ? ? ?MASS_7.3-14 > [5] plyr_1.6 ? ? ? ? ? stringr_0.5 ? ? ? ?tools_2.14.0 ? ? ? XML_3.4-3 > [9] zlibbioc_0.1.8 >> > > -- > Dr. Kathi Zarnack > Luscombe Group > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD, UK > tel +44 1223 494 526 > > _______________________________________________ > 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 >