brucemoran/1359_perry_epic

1359_Perry_EPIC Array Analysis

Run the EPIC array analysis for Silva et al. (in submission)

Getting started

In a Linux environment simply issue the commands (N.B. for OSX you can use 'greadlink' via Homebrew):

git clone https://github.com/brucemoran/1359_Perry_EPIC
sh ./scripts/run_RnBeads-probeEMR-corrMatrix.sh \
   "$(readlink -e ./1359_Perry_EPIC)" \
   "$(readlink -e ./1359_Perry_EPIC/scripts)" \
   "1359_Perry_EPIC" \
   "$(readlink -e ./1359_Perry_EPIC/data/sample_annotation.csv)"

This downloads the raw IDAT files (~440MB), EPIC array annotation (~570MB), and runs RnBeads, and our full analysis. To run the R analysis, and not the full RnBeads analysis from IDATs, include a fifth input to the shell script

Prerequisites

You will need a copy of R installed (3.5.0 tested and working, other versions unknown), as well as required R packages. These can be installed using the the script specified below. N.B. that this uses BiocManager, which may not be available to older versions of R.

Rscript ./scripts/prerequisites.R