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matthew.bashton
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@matthewbashton-12986
Last seen 7.6 years ago
Those using OmicCircos should be aware that the UCSC.hg19.chr
dataframe provided with this package actually contains hg18 cytoband co-ordinates:
library(OmicCircos) data(UCSC.hg18.chr) data(UCSC.hg19.chr) identical(UCSC.hg18.chr, UCSC.hg19.chr) [1] TRUE
The correct co-ordinates can be confirmed via cross referencing:
hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz
With the two dataframes provided.
sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] OmicCircos_1.14.0 GenomicRanges_1.28.1 GenomeInfoDb_1.12.0 IRanges_2.10.0 S4Vectors_0.14.0 BiocGenerics_0.22.0 BiocInstaller_1.26.0 loaded via a namespace (and not attached): [1] zlibbioc_1.22.0 compiler_3.4.0 XVector_0.16.0 tools_3.4.0 GenomeInfoDbData_0.99.0 RCurl_1.95-4.8 bitops_1.0-6