Analysis of Methylation for Crohn's Disease

Overview

The repo analyzes DNA methylation in Adipocyte Tissues for Crohn's Disease, along with demonstrating the usage of permutation tests and parallel computing.

Navigation

• DNA_Crohn.R: The script of analysis.
• DNA_Crohn.Rmd, results.pdf: Files producing the results.

Installation

Data can be downloaded using the command line.
Details of the data and experiment can be found on the Gene Expression Omnibus website.

wget -O - ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138311/matrix/GSE138311_series_matrix.txt.gz | gunzip -c > matrix.txt

To run the R script, the following packages should be pre-installed in the IDE.

install.packages('tidyverse')
install.packages('data.table')
install.packages('parallel')
install.packages('future')

Remark

The repo is a revised work of the course Stats506 Computational Methods and Tools in Statistics taught by Dr. Henderson.