asd_meth

Analysis of methylation data of twins where one or both of the twins has autism spectrum disorder. This is a longitudinal study that includes newborm blood spots, blood at ASD assessment, and buccal swabs in later life.

Requirements

Ubuntu 20+ with Docker installed. 64GB or more RAM. 8 CPU threads or more.

Steps to run

1. Pull the docker image which has all the necessary software and data:

docker pull mdziemann/asd_meth

2. Start up an interactive shell in the docker container:

docker run -it asd_meth /bin/bash

3. Run the master script:

Rscript main.R

The master script will subsequently execute 6 R markdown scripts:

• asd_covariates.Rmd

• limma_blood.Rmd, limma_buccal.Rmd, limma_guthrie.Rmd

• downstream1_ados.Rmd

• downstream2_ados.Rmd

4. Copy the analysis directory from the container to the host machine. It will contain all the results in the HTML and PDF files which includes figures and tables.

docker cp $(docker ps -alq):/asd_meth .

Reporting problems

Please use github issues to report bugs. Include any error messages or other relevant information to facilitate troublieshooting.