plotgardenerData

Nicole Kramer

Sample experimental data

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:

library(plotgardenerData)
data("IMR90_HiC_10kb")

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.

Sample raw files

Small, example .bigwig and .hic files are included in the inst/extdata directory to demonstrate the functionality of the plotgardener functions readBigwig and readHic:

bwFile <- system.file("extdata/test.bw", package = "plotgardenerData")
hicFile <- system.file("extdata/test_chr22.hic", package = "plotgardenerData")

Session info

sessionInfo()
## R version 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 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_1.3.0
## 
## 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_1.38      sass_0.4.1