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 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] plotgardenerData_1.0.0
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## loaded via a namespace (and not attached):
## [1] digest_0.6.28 R6_2.5.1 jsonlite_1.7.2 magrittr_2.0.1
## [5] evaluate_0.14 rlang_0.4.12 stringi_1.7.5 jquerylib_0.1.4
## [9] bslib_0.3.1 rmarkdown_2.11 tools_4.1.1 stringr_1.4.0
## [13] xfun_0.27 yaml_2.2.1 fastmap_1.1.0 compiler_4.1.1
## [17] htmltools_0.5.2 knitr_1.36 sass_0.4.0