Question: OmicCircos: included UCSC.hg19.chr dataframe is actually hg18 cytobands
0
gravatar for matthew.bashton
2.4 years ago by
matthew.bashton0 wrote:

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 

 

data bug omiccircos hg19 hg18 • 469 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by matthew.bashton0
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