This package provides subsets of publicly available Hi-C, ChIP-seq, DNA looping, GWAS, and COVID-19 datasets. The genomic datasets are all in reference to the hg19 genome build. These datasets are included in the data directory and can be loaded with the data() call:
The full versions of these datasets can be found at the citations provided in each data documentation file (e.g. ?IMR90_HiC_10kb).
The plotgardener vignettes detail how to visualize these datasets.
Small, example .bigwig and .hic files are included in the inst/extdata directory to demonstrate the functionality of the plotgardener functions readBigwig and readHic:
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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## time zone: America/New_York
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] plotgardenerData_1.8.0
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## loaded via a namespace (and not attached):
## [1] digest_0.6.33 R6_2.5.1 fastmap_1.1.1 xfun_0.40
## [5] cachem_1.0.8 knitr_1.44 htmltools_0.5.6.1 rmarkdown_2.25
## [9] cli_3.6.1 sass_0.4.7 jquerylib_0.1.4 compiler_4.3.1
## [13] tools_4.3.1 evaluate_0.22 bslib_0.5.1 yaml_2.3.7
## [17] rlang_1.1.1 jsonlite_1.8.7