Introduction and setup

Last updated on 2024-11-19 | Edit this page

Overview

Questions

  • Am I using the correct version of R for this lesson?
  • Why does my version of R matter?
  • How do I obtain the files that are used in this lesson?

Objectives

  • Ensure that participants are using the correct version of R to reproduce exactly the contents of this lesson.
  • Download the example files for this lesson.

Version of R

This lesson was developed and tested with R version 4.4.2 (2024-10-31).

Take a moment to launch RStudio and verify that you are using R version 4.4.x, with x being any patch version, e.g. 4.4.2.

R 

R.version.string

OUTPUT 

[1] "R version 4.4.2 (2024-10-31)"

This is important because Bioconductor uses the version of R running in the current session to determine the version of Bioconductor packages that can be installed in the R library associated with the current R session. Using a different version of R while following this lesson may lead to unexpected results.

Download files

Several episodes in this lesson rely on example files that participants need to download.

Run the code below programmatically create a folder called data in the current working directory, and download the lesson files in that folder.

R 

dir.create("data", showWarnings = FALSE)
download.file(
    url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/master/data/TrimmomaticAdapters/TruSeq3-PE-2.fa", 
    destfile = "data/TruSeq3-PE-2.fa"
)
download.file(
    url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/master/data/ActbGtf/actb.gtf", 
    destfile = "data/actb.gtf"
)
download.file(
    url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/master/data/ActbOrf/actb_orfs.fasta", 
    destfile = "data/actb_orfs.fasta"
)
download.file(
  url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/counts.csv",
  destfile = "data/counts.csv"
)
download.file(
  url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/gene_metadata.csv",
  destfile = "data/gene_metadata.csv"
)
download.file(
  url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/sample_metadata.csv",
  destfile = "data/sample_metadata.csv"
)

Note

Ideally, participants might want to create a new RStudio project and download the lesson files in a sub-directory of that project.

Using an RStudio project sets the working directory to the root directory of that project. As a consequence, code is executed relative to that root directory, often avoiding the need for using absolute file paths to import/export data from/to files.

Key Points

  • Participants will only be able to install the version of Bioconductor packages described in this lesson and reproduce their exact outputs if they use the correct version of R.
  • The files used in this lesson should be downloaded in a local path that is easily accessible from an R session.