Authors: Gabriel J. Odom, Suky Martinez, Tiago Silva, Ingrid Gonzalez, Fernanda Veitzman, Lissette Gomez, Jermaine Jones, and Lily Wang
Event: coMethDMR Workshop for BioC2022 in Seattle, WA
This workshop shows how to use the coMethDMR:: package for R to detect co-methylated regions of the genome which may be associated with a phenotype of interest. This workshop shows an application related to heroin use. Our paper is here: https://doi.org/10.1093/nar/gkz590. Our pacakge website shows other examples: https://transbioinfolab.github.io/coMethDMR/.
You will need the following packages and data to run the examples in this workshop:
- The
coMethDMRpackage - A list of genomic regions with close-by CpGs, for Illumina 450k or EPIC arrays
- the coMethDMR_data repository includes pre-calculated lists of these regions for certain parameter values
- for this workshop, you will need the file
"EPIC_10b4_Gene_3_200.rds"in thedata/directory. The original source for this file is here: https://github.com/TransBioInfoLab/coMethDMR_data/blob/main/data/EPIC_10b4_Gene_3_200.rds
- Sample-matched phenotype and DNA methylation data (example semi-synthetic data in
data/) - A cup of coffee (or tea) and a little bit of patience
- Fork and download this repository
- Install
coMethDMRfrom Bioconductor with the following commands:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("coMethDMR")
- Install human genome data packages:
BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
BiocManager::install("sesameData")
- For various supplemental components of the workshop, install the following packages:
# General workflow
install.packages("tidyverse")
# Pretty tables of results
install.packages("kableExtra")
# Graphics and Wrangling Genomic Data
install.packages("corrplot")
BiocManager::install("pathwayPCA")
To see the workshop with rendered results (powered by GitHack), please visit: