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Taiki Tsutsui
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10
@taiki-tsutsui-14286
Last seen 5.4 years ago
Dear all,
I am new in this field. I am trying to visualizing genomic element using Gviz following its tutorial linked below.
https://www.bioconductor.org/help/course-materials/2012/BiocEurope2012/GvizEuropeanBioc2012.pdf
When I try IdeogramTrack command, I got a error message like following.
Perhaps I do not understand the clearly how Gviz works. Help is greatly appreciated!
> itr <- IdeogramTrack(genome="mm9", chromosome="chr1") Error in UseMethod("xmlNamespaceDefinitions") : no applicable method for 'xmlNamespaceDefinitions' applied to an object of class "NULL"
My condition
> sessionInfo() R version 3.4.1 (2017-06-30) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 7 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=Japanese_Japan.932 LC_CTYPE=Japanese_Japan.932 [3] LC_MONETARY=Japanese_Japan.932 LC_NUMERIC=C [5] LC_TIME=Japanese_Japan.932 attached base packages: [1] grid parallel stats4 stats graphics grDevices utils [8] datasets methods base other attached packages: [1] XML_3.98-1.9 AnnotationHub_2.8.2 Gviz_1.20.0 [4] GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.4 [7] S4Vectors_0.14.6 BiocGenerics_0.22.0