Installation

Install CAMDAC

From the R console, install CAMDAC from github:

install.packages("remotes")
remotes::install_github("VanLoo-lab/CAMDAC")

Download pipeline reference files

CAMDAC requires custom annotation files for RRBS and WGBS analysis, available at the Zenodo repository: (10565423). An R convenience function is provided to download these files:

CAMDAC::download_pipeline_files(bsseq = "rrbs", directory = "./refs")
CAMDAC::download_pipeline_files(bsseq = "wgbs", directory = "./refs")

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

Reference file search priority

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

External dependencies

CAMDAC-RRBS

  • None

CAMDAC WGBS

  • java: To run CAMDAC on WGBS data, we leverage Battenberg which requires the java command-line utility. Download Java from https://openjdk.org/.