Installation

Install CAMDAC

From within R, install CAMDAC from github:

library(remotes)
remotes::install_github("VanLoo-lab/CAMDAC@wgbs")

Prepare pipeline files

CAMDAC requires pre-made annotation files to run, which you can download by running:

CAMDAC::download_pipeline_files("wgbs", directory="./pipeline_files")

Now, you’re ready to run CAMDAC! Next, see vignette("pipeline").

Are there external dependencies?

CAMDAC runs Battenberg to call copy number variants in WGBS mode. This requires requires the java command-line utility to be available in the system path. Otherwise, you can download Java from https://openjdk.org/.

How does CAMDAC find pipeline files?

CAMDAC searches for pipeline files in the following order:

  1. A directory passed when creating the config object (see CamConfig())
  2. The location defined by the environment variable CAMDAC_PIPELINE_FILES.
  3. The current working directory

We recommend that you set the environment variable CAMDAC_PIPELINE_FILES to the directory where you downloaded the files. This will allow CAMDAC to find the files automatically whenever you load R.

From a Unix terminal: > echo “CAMDAC_PIPELINE_FILES=$(realpath R)” >> ~/.Renviron

I have an error when downloading pipeline files

If the download command fails (e.g. due to a firewall), you can manually download the files from the endpoints listed in inst/extdata/pipeline_files_urls.txt. Data are stored as tar.gz files, therefore you will need to unpack them with the command tar -xvzf <file>.