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 4.2.0 RC (2022-04-19 r82224)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-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_1.2.0
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## loaded via a namespace (and not attached):
## [1] digest_0.6.29 R6_2.5.1 jsonlite_1.8.0 magrittr_2.0.3
## [5] evaluate_0.15 stringi_1.7.6 rlang_1.0.2 cli_3.3.0
## [9] jquerylib_0.1.4 bslib_0.3.1 rmarkdown_2.14 tools_4.2.0
## [13] stringr_1.4.0 xfun_0.30 yaml_2.3.5 fastmap_1.1.0
## [17] compiler_4.2.0 htmltools_0.5.2 knitr_1.39 sass_0.4.1