setup.md

layout	title
page	Setup

It's usually recommended that course instructors provide a virtual environment with software and data available. However this page includes instructions to set up for the lessons. This should take about an hour to run, depending on the speed of your computer, your internet connection, and any packages you have installed already. You'll need to install R 4.0 or later.

The following code will download the data and install the libraries used in the current version of this lesson:

install.packages("BiocManager")
download.file(
    "https://raw.githubusercontent.com/carpentries-incubator/high-dimensional-stats-r/gh-pages/dependencies.csv",
    destfile = 'dependencies.csv'
)
table <- read.table('dependencies.csv')
BiocManager::install(table[[1]])

dir.create("data", showWarnings = FALSE)
data_files <- c(
    "cancer_expression.rds",
    "coefHorvath.rds",
    "methylation.rds",
    "scrnaseq.rds",
    "prostate.rds"
)
for (file in data_files) {
    download.file(
        url = file.path(
            "https://raw.githubusercontent.com/carpentries-incubator/high-dimensional-stats-r/gh-pages/data",
            file
        ),
        destfile = file.path("data", file)
    )
}

On Linux systems, part of the above may fail due to the bluster package and you may receive error messages after running BiocManager::install(table[[1]]), indicating that the package igraph was not installed successfully.

Detailed installation instructions for igraph can be found at https://r.igraph.org/, but the following workaround code may resolve the issue:

install.packages('igraph', repos=c(igraph = 'https://igraph.r-universe.dev', 
                                   CRAN = 'https://cloud.r-project.org'))
                                   
BiocManager::install('bluster')

{% include links.md %}