Question

Gviz problem with chr16

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Dear Gviz developers, We have come across an issue while visualizing chromosome 16 of the human genome hg19 using IdeogramTrack and plotTracks. Plotting chr16 produces the following error: Error in lcS[[as.numeric(j) - 1]] : subscript out of bounds while this does not happen with other chromosomes. Please see the minimal example attached below. ##### beginning of script ###### # produces an error with chr16 (but not with other chromosomes) library(Gviz) library(GenomicRanges) data(cpgIslands) cg = GRanges(seqnames = "chr16",ranges = ranges(cpgIslands)) chr <- as.character(unique(seqnames(cg))) gen = "hg19" atrack <- AnnotationTrack(cg, name = "CpG") itrack <- IdeogramTrack(genome = "hg19", chromosome = chr) gtrack <- GenomeAxisTrack() plotTracks(list(itrack, gtrack, atrack)) ##### end of script ###### We believe this must be an error in the plotting engine and/or the chromosome data. Thank you for looking into this, best wishes, Adam Novak Sophia Genetics SA ps. please CC me in the reply as I'm not subscribed to the list - thank you -- output of sessionInfo(): R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (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] parallel grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.12.2 IRanges_1.18.0 BiocGenerics_0.6.0 [4] Gviz_1.4.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.22.5 Biobase_2.20.0 biomaRt_2.16.0 [4] Biostrings_2.28.0 biovizBase_1.8.0 bitops_1.0-5 [7] BSgenome_1.28.0 cluster_1.14.4 colorspace_1.2-2 [10] DBI_0.2-6 dichromat_2.0-0 GenomicFeatures_1.12.1 [13] Hmisc_3.10-1.1 labeling_0.1 lattice_0.20-15 [16] munsell_0.4 plyr_1.8 RColorBrewer_1.0-5 [19] RCurl_1.95-4.1 Rsamtools_1.12.2 RSQLite_0.11.3 [22] rtracklayer_1.20.2 scales_0.2.3 stats4_3.0.0 [25] stringr_0.6.2 tools_3.0.0 XML_3.95-0.2 [28] zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

Genetics Gviz Genetics Gviz • 1.2k views

ADD COMMENT • link updated 11.8 years ago by florian.hahne@novartis.com ★ 1.6k • written 11.8 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2013-05-13

Hi Adam, thanks for reporting this bug. A fixed version should be available in the next couple of days as soon as it passes the build system (1.4.2 in release and 1.5.3 in devel) Florian Florian Hahne Novartis Institute For Biomedical Research Translational Sciences / Preclinical Safety / PCS Informatics Expert Data Integration and Modeling Bioinformatics CHBS, WKL-135.2.26 Novartis Institute For Biomedical Research, Werk Klybeck Klybeckstrasse 141 CH-4057 Basel Switzerland Phone: +41 61 6967127 Email : florian.hahne at novartis.com On 5/10/13 8:53 PM, "Adam Novak [guest]" <guest at="" bioconductor.org=""> wrote: > >Dear Gviz developers, > >We have come across an issue while visualizing chromosome 16 of the human >genome hg19 using IdeogramTrack and plotTracks. Plotting chr16 produces >the following error: > >Error in lcS[[as.numeric(j) - 1]] : subscript out of bounds > >while this does not happen with other chromosomes. Please see the minimal >example attached below. > >##### beginning of script ###### ># produces an error with chr16 (but not with other chromosomes) >library(Gviz) >library(GenomicRanges) >data(cpgIslands) >cg = GRanges(seqnames = "chr16",ranges = ranges(cpgIslands)) >chr <- as.character(unique(seqnames(cg))) >gen = "hg19" >atrack <- AnnotationTrack(cg, name = "CpG") >itrack <- IdeogramTrack(genome = "hg19", chromosome = chr) >gtrack <- GenomeAxisTrack() >plotTracks(list(itrack, gtrack, atrack)) >##### end of script ###### > >We believe this must be an error in the plotting engine and/or the >chromosome data. > >Thank you for looking into this, best wishes, > >Adam Novak >Sophia Genetics SA > >ps. please CC me in the reply as I'm not subscribed to the list - thank >you > > -- output of sessionInfo(): > >R version 3.0.0 (2013-04-03) >Platform: x86_64-apple-darwin10.8.0 (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] parallel grid stats graphics grDevices utils datasets >[8] methods base > >other attached packages: >[1] GenomicRanges_1.12.2 IRanges_1.18.0 BiocGenerics_0.6.0 >[4] Gviz_1.4.1 > >loaded via a namespace (and not attached): > [1] AnnotationDbi_1.22.5 Biobase_2.20.0 biomaRt_2.16.0 > [4] Biostrings_2.28.0 biovizBase_1.8.0 bitops_1.0-5 > [7] BSgenome_1.28.0 cluster_1.14.4 colorspace_1.2-2 >[10] DBI_0.2-6 dichromat_2.0-0 GenomicFeatures_1.12.1 >[13] Hmisc_3.10-1.1 labeling_0.1 lattice_0.20-15 >[16] munsell_0.4 plyr_1.8 RColorBrewer_1.0-5 >[19] RCurl_1.95-4.1 Rsamtools_1.12.2 RSQLite_0.11.3 >[22] rtracklayer_1.20.2 scales_0.2.3 stats4_3.0.0 >[25] stringr_0.6.2 tools_3.0.0 XML_3.95-0.2 >[28] zlibbioc_1.6.0 > >-- >Sent via the guest posting facility at bioconductor.org.