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 4.4.0 RC (2024-04-16 r86468)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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## 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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] plotgardenerData_1.11.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.35 R6_2.5.1 fastmap_1.1.1 xfun_0.43
## [5] cachem_1.0.8 knitr_1.46 htmltools_0.5.8.1 rmarkdown_2.26
## [9] lifecycle_1.0.4 cli_3.6.2 sass_0.4.9 jquerylib_0.1.4
## [13] compiler_4.4.0 tools_4.4.0 evaluate_0.23 bslib_0.7.0
## [17] yaml_2.3.8 rlang_1.1.3 jsonlite_1.8.8