DNAm Age Tutorial

This repository contains variation of the "R Tutorials" software at: https://horvath.genetics.ucla.edu/html/dnamage/

"[...] the original standard analysis is implemented in the following R software tutorial that shows how to calculate DNAm age based on Illumina DNA Infinium 27K or 450K data is available. These R scripts carry out normalization steps and show how to estimate DNAm age."

Based on the number of CpG sites selected (AdditionalFile3.csv), I believe this code corresponds to the work in:

Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol 14, 3156 (2013). https://doi.org/10.1186/gb-2013-14-10-r115

First time set up

This step installs dependencies (it takes a while to compile up the binaries). You'll need R and development tools (probably gcc).

$ R
> if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
> BiocManager::install()
> BiocManager::install("impute")
> BiocManager::install("preprocessCore")
> BiocManager::install("GO.db")
> BiocManager::install("AnnotationDbi")
> BiocManager::install("RPMM")
> install.packages("sqldf")
> install.packages("WGCNA")

Run

$ R
> source("main.r")

I used R version 4.0.2.