TENET.ExperimentHub

ExperimentHub package containing datasets for use in the TENET package's function examples and vignettes

Introduction

The TENET.ExperimentHub package contains 6 datasets for use in the TENET package's examples and vignettes. These datasets include an example MultiAssayExperiment object with matched gene expression and DNA methylation data from a subset of both tumor (case) and adjacent normal (control) samples in The Cancer Genome Atlas (TCGA)'s breast adenocarcinoma (BRCA) cohort with essential information used in all TENET functions, an example GRanges object produced by the TENET step1MakeExternalDatasets function, a SummarizedExperiment object with example purity data to pass to the TENET step2GetDifferentiallyMethylatedSites function, a data frame with example patient clinical data (matching the data in the example MultiAssayExperiment object), and two additional GRanges objects containing example peak and topologically associating domain (TAD) data, respectively. Where applicable, all datasets are aligned to the hg38 human genome.

Acquiring and installing TENET.ExperimentHub

R 4.5 or a newer version is required.

On Ubuntu 24.04, successful installation required several additional packages. They can be installed by running the following command in a terminal:

sudo apt-get install r-base-dev libcurl4-openssl-dev libfreetype-dev libfribidi-dev libfontconfig-dev libharfbuzz-dev libtiff-dev libxml2-dev libssl-dev

No dependencies other than R are required on macOS or Windows.

Two versions of this package are available.

To install the stable version from Bioconductor, start R and run:

## Install BiocManager, which is required to install packages from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("TENET.ExperimentHub")

The development version containing the most recent updates is available from our GitHub repository.

To install the development version from GitHub, start R and run:

## Install prerequisite packages to install the development version from GitHub
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")
}

BiocManager::install(version = "devel")
BiocManager::install("rhielab/TENET.ExperimentHub")

Loading TENET.ExperimentHub

To load the TENET.ExperimentHub package, start R and run:

library(TENET.ExperimentHub)

Using the included datasets