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 Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## 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_1.13.0
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.37 R6_2.5.1 fastmap_1.2.0 xfun_0.48
## [5] cachem_1.1.0 knitr_1.48 htmltools_0.5.8.1 rmarkdown_2.28
## [9] lifecycle_1.0.4 cli_3.6.3 sass_0.4.9 jquerylib_0.1.4
## [13] compiler_4.5.0 tools_4.5.0 evaluate_1.0.1 bslib_0.8.0
## [17] yaml_2.3.10 rlang_1.1.4 jsonlite_1.8.9