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 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] plotgardenerData_1.4.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.30 R6_2.5.1 jsonlite_1.8.3 magrittr_2.0.3
## [5] evaluate_0.17 stringi_1.7.8 rlang_1.0.6 cachem_1.0.6
## [9] cli_3.4.1 jquerylib_0.1.4 bslib_0.4.0 rmarkdown_2.17
## [13] tools_4.2.1 stringr_1.4.1 xfun_0.34 yaml_2.3.6
## [17] fastmap_1.1.0 compiler_4.2.1 htmltools_0.5.3 knitr_1.40
## [21] sass_0.4.2