In PhanstielLab/plotgardenerData: Datasets and test data files for the plotgardener package

knitr::opts_chunk$set(echo = TRUE)

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()

PhanstielLab/plotgardenerData documentation built on June 15, 2024, 10:38 p.m.